Boutique hotels in Thousand Islands

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Top-rated boutique hotels in Thousand Islands

Guests agree: these boutique hotels are highly rated for location, cleanliness, and more.

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Top guest favorite

A spacious sleeping area is enhanced by a wooden ceiling, creating an inviting ambiance. Large glass doors open to a balcony, allowing natural light to fill the room. A bedside table holds a potted plant, and a soft area rug complements the flooring.

Hotel room in Clayton

4.94 out of 5 average rating, 109 reviews

Island Bay Waterfront Captains Suite

Our one of a kind location is nested right on the edge of the Village of historic Clayton, with our upstairs studio style suite overlooking our waterfront lawn and dock area, unique with great views and centrally located right in the heart of the 1000 islands area. New from top to bottom with all amenities and private balcony with dockage right in front available, a boaters dream! King size bedroom with Full kitchenette with all the essentials with full 2 couch living area with modern amenities!

Superhost

A spacious bedroom features a large, neutral-toned bed and matching light wood nightstands. A decorative woven wall piece is positioned above the bed, with a soft area rug delineating the space. Natural light fills the room, aided by minimal window coverings.

Hotel room in Clayton

4.73 out of 5 average rating, 11 reviews

Island Bayside "Getaway Grotto" room

Our ”Fisherman’s Grotto” unit is right on the edge of the Village of historic Clayton, our downstairs unit overlooks our waterfront lawn and dock, unique with great views and located right in the heart of the 1000 islands area. New from top to bottom with all amenities, Smart tv, WiFi, heated towel rack,deck and patio, dockage right in front available for extra charge, a boaters dream! Super comfortable King size bed with all the essentials, enjoy a hot Keurig coffee as well as microwave/fridge

The cozy bedroom features a queen-sized bed with a quilted gray coverlet. A wooden cabinet and coffee maker are positioned nearby. The room is illuminated by two table lamps on either side. A large area rug with floral patterns covers the dark wooden floor.

Hotel room in Gananoque

4.92 out of 5 average rating, 38 reviews

The Frederick Suite – Stonewater Manor B&B

Welcome to the Frederick Suite at the Stonewater Manor B&B. We are located 2 minutes from the Gananoque Boat Lines Thousand Islands Tours dock, the Arthur Child and Antique Boat Museums, the beach and Joel Stone Park and the 1000 Islands Playhouse. Our Frederick Suite is a cozy room that has good views of the Gananoque harbour and St. Lawrence River. This season, as a more Covid friendly option, we are offering continental breakfasts served to your room, included in the rate for your stay.

Guest favorite

A well-lit room features a large window with a view of greenery, complemented by a wooden ceiling. A compact kitchenette is equipped with a coffee maker and a small refrigerator. A comfortable chair is positioned near the window, and a cozy bed adds to the inviting space.

Hotel room in Clayton

4.9 out of 5 average rating, 99 reviews

Island Bay Waterfront -River View Room

Welcome to the Island Bay stays! Right on the edge of Historic Clayton NY, enjoy our super newly renovated waterfront “Aparthotel” style stay! Our elevated well insulted rooms and suite apartments have all the newest amenities to keep you connected and even better yet, disconnecting and relaxing to take in the 1000 islands by land or boat! Centrally located, less than a 10 min walk to downtown, Dockage available, with boat ramp and Clayton Marina and boat rentals right across the way!

Superhost

A spacious guest room is presented with vibrant red wallpaper and traditional furnishings. A king size bed with decorative linens is framed by tall posts. An ornate fireplace, accompanied by a red armchair, adds charm. A vintage rug covers the wood floor, contributing to the room's historic ambiance.

Hotel room in Gananoque

4.84 out of 5 average rating, 43 reviews

The King's Room - Chrysler House Heritage Inn

Chrysler House is a unique 6800 sq ft Georgian-Victorian style mansion built in 1826. It is located in the historical heart of Gananoque and the beautiful 1000 Islands; just minutes away from the waterfront, marina, boat line, beach, downtown shopping and restaurants. The King's Room features a king size bed and private bathroom with jet tub and shower *located down the hall from the bedroom*. It overlooks the Gananoque river and bridge.

Guest favorite

A spacious bedroom features a classic wooden sleigh bed covered with a soft beige duvet. Natural light streams through large windows adorned with floral curtains, highlighting a decorative dresser with floral arrangements. A cozy seating area includes an antique chair on a patterned rug.

Hotel room in Gananoque

4.88 out of 5 average rating, 48 reviews

The Garden Room - Chrysler House Heritage Inn

Chrysler House is a unique 6800 sq ft Georgian-Victorian style mansion built in 1826. It is located in the historical heart of Gananoque and the beautiful 1000 Islands; just minutes away from the waterfront, marina, boat line, beach, downtown shopping and restaurants. The Garden Room is light and spacious and features a luxurious king size bed, ensuite bathroom with jet tub and walk-in shower, and private entrance onto the backyard deck.

Superhost

A well-maintained garden showcases a variety of colorful flowers, including orange and yellow blooms. A patio area with seating is visible in front of the mansion's entrance, surrounded by lush greenery and a welcoming stone pathway leading to the main door.

Hotel room in Gananoque

4.76 out of 5 average rating, 49 reviews

The Peninsula Room - Chrysler House Heritage Inn

Chrysler House is a unique 6800 sq ft Georgian-Victorian style mansion built in 1826. It is located in the historical heart of Gananoque and the beautiful 1000 Islands; just minutes away from the waterfront, marina, boat line, beach, downtown shopping and restaurants. The Peninsula Room is a light and cozy room that features a twin bed and an ensuite half bathroom. A private shower is available outside of the bedroom on the first floor.

Superhost

A modern suite features two queen beds with dark blue throws. A sleek ambient fireplace is centered in the room, complemented by a minimalist wooden panel wall. A 75" TV is mounted above, with a small plant enhancing the decor.

Hotel room in Prince Edward

4.67 out of 5 average rating, 3 reviews

Cribs on Main-Picton Hotel - Suite 5

This 447 sq ft suite features two queen beds for group travellers or those who just want their own space. Suite 5 has a walk in shower with a large window to the bedroom (privacy blind), allowing maximum light to flow through, a separate water closet, radiant floor heating, ambient fireplace, work station, 75" smart tv, make-up station, and mini-bar. The bathroom area has a room dividing curtain for added privacy from the sleeping area.

Guest favorite

A charming bedroom features a double bed with a classic wooden headboard, accompanied by an elegant green chair. Decorated with floral wallpaper and rich tones, it showcases a small bedside table and a vintage area rug, providing a warm and inviting space.

Hotel room in Gananoque

4.88 out of 5 average rating, 75 reviews

The Heritage Room - Chrysler House Heritage Inn

Chrysler House is a unique 6800 sq ft Georgian-Victorian style mansion built in 1826. It is located in the historical heart of Gananoque and the beautiful 1000 Islands; just minutes away from the waterfront, marina, boat line, beach, downtown shopping and restaurants. The Heritage Room features a double bed and twin bed, and a three piece ensuite bathroom with walk-in shower. It is full of Victorian charm and overlooks the back garden.

Superhost

A cozy bedroom features a wooden bed with soft gray bedding and decorative pillows. Natural light fills the room through a large window adorned with blue patterned curtains. A small bedside lamp and art pieces on the walls add to the inviting atmosphere.

Hotel room in Gananoque

4.82 out of 5 average rating, 39 reviews

The Maritime Room - Chrysler House Heritage Inn

Chrysler House is a unique 6800 sq ft Georgian-Victorian style mansion built in 1826. It is located in the historical heart of Gananoque and the beautiful 1000 Islands; just minutes away from the waterfront, marina, boat line, beach, downtown shopping and restaurants. The Maritime Room features a king size bed and a three piece ensuite bathroom with walk-in shower. It is a light and cozy room that overlooks the back garden.

Superhost

A cozy living area features a decorative fireplace with an elegant mantel. A patterned area rug lies on the hardwood floor, complementing a seating arrangement that includes a sofa and two chairs surrounding a round table. Natural light enters through the window, framed by soft drapes.

Hotel room in Gananoque

4.79 out of 5 average rating, 29 reviews

The Painter's Suite - Chrysler House Heritage Inn

Chrysler House is a unique 6800 sq ft Georgian-Victorian style mansion built in 1826. It is located in the historical heart of Gananoque and the beautiful 1000 Islands; just minutes away from the waterfront, marina, boat line, beach, downtown shopping and restaurants. The spacious Painter's Suite features a queen bed, private living room, and an ensuite bathroom. It overlooks the Gananoque river and back garden.

Guest favorite

A spacious bedroom features a luxurious king size bed with crisp white linens and navy accents. Natural light filters through the large window, which offers a view of Main Street. Soft wood tones and contemporary design elements contribute to a calming atmosphere.

Hotel room in Prince Edward

4.88 out of 5 average rating, 17 reviews

Cribs on Main-Picton Hotel - Suite 3

Suite 3 boasts 370 sq ft, featuring a luxurious king size bed, radiant heated floors, and a generous rainfall walk-in shower with a frosted window to the bedroom for added light. Enjoy the convenience of a separate water closet, work station, 75" flatscreen TV, and a mini-bar. With a view of Main Street, this room blends fresh, modern styling with cozy County comfort. Relax in luxury.