Let KAYAK do the searching
Based on KAYAK hotel searches, the most popular destination is Friday Harbor (99% of total searches to San Juan Island). The next most popular destination is Roche Harbor (1%).
If you would like to treat yourself during your stay on San Juan Island, you can always book one of the several luxury hotels that are available. The Snug Harbor Resort is a nice choice that offers travelers access to their decks, views of the water, and BBQing areas.
Those who are hoping to play a game or two of golf during their stay on San Juan Island can always book a hotel that is just a short distance from the San Juan Golf & Tennis Club. When you stay at the stylish Tucker House Inn, you will be less than a 15min drive from the course.
A nice way to treat yourself and relax during your vacation on San Juan Island is by staying at a hotel that has its own on-site spa. The Earthbox Inn & Spa is a great place to stay that can be found right in the heart of Friday Harbor and offers a variety of massage and facial services.
To stay at a hotel that is placed directly on the water, you have a few different options. You can always book the Bird Rock Hotel, which is located in Friday Harbor and is right next to the ocean.