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My wife and I took a flying vacation up there a couple years ago for our 10yr anniversary (in a C152... had to ship our camping gear). In Friday Harbor (San Juan Island), we stayed at Kirk House B&B (Kirkhouse.net) which was a 5 min walk from the airport, and they picked us up on arrival so we didn't have to lug our stuff. They took very good care of us and the breakfast was great. Its pretty small, just 3 or 4 rooms, so book early. I took Debbie, one of the owners, up on her first aerial tour of the islands, which hopefully made her even more enthusiastic about hosting pilots. One day we flew over to Lopez Island and had a guy from the bike shop meet us as the airport with a tandem bike. After a couple hours cruising around, we ended up back at the shop and he drove us back to the airport (gave him a good tip for sure!). Great fun and way better than a full day of ferry ride to do the same biking.
After a 2 night stay, we went out for a 3 day, 2 night sea kayaking trip with Outdoor Odysseys (outdoorodysseys.com) who I highly recommend even for just day trips if you aren't up for a bigger adventure. Don't try paddling the San Juans without a lot of experience because the tidal currents can be brutal.
From there we transferred to Orcas Island where we spend one night at Kangaroo House B&B (kangaroohouse.com), also a short walk from the airport and they'll give you a ride. Again a really nice place, great breakfast, and a nice, private outdoor hot tub. They only had a room for one night, plus we wanted to splurge for our anniversary, so we rented a car for a couple days and transferred to Turtleback Farm Inn (turtlebackinn.com) which was amazing (and expensive). Great breakfast delivered to the room if you like, nice grounds to wonder, orchard to eat apples and pears off the trees, etc. I'd recommend the Orchard House which is a newer building with bigger rooms. Orcas is the biggest island, so having a car is nice for exploring, especially after flying over to preview where you want to go. For a more crunchy granola budget experience, check out Doe Bay, where we camped many years prior.
All-in-all, a great memorable trip, with great weather right up until the day we had to fly back to Portland. The entire Seattle area was socked in down low, so we had to make several stops to wait for the clouds and/or to work our way around. An RV could have easily climbed above the slop from the San Juans that were clear.
Other options nearby that we didn't explore are, of course, Victoria & Vancouver BC, the Seattle Museum of Flight, etc. Have a great trip!