We decided that we would spend all of our time (4 nights) exploring San Juan Island which is the largest. There are many options regarding how to get there and of all of them, I do not suggest the state ferry - that's what we did and while it's definitely easiest on the budget, we encountered major problems in both directions. The Victoria Clipper makes non-stop trips from Seattle to Friday Harbor and there are flightseeing options for those who don't mind small aircraft.
There are lots of wonderful places to stay throughout this island all for different reasons. We chose the Lakedale Resort which has a central location where we could try "glamping". This was perfect for us as it was sort of like summer camp for families but not in a crowded touristy way. The little canvas tents with wooden floors, cozy queen beds and electricity were quite a step up from regular camping. Not to mention the spotless shared bathhouse where you could shower and wash up after biking, hiking or playing in the lake. http://www.lakedaleresort.com/
From our homebase where we spent very little time, we could explore both Roche Harbor and Friday Harbor easily. Roche Harbor is a quaint little sea port with a couple of wonderful dining options, shops, boat rentals and history - the Hotel Harobuilt in the late 1800's is said to be haunted! (Why stay there when there are the new luxurious McMillin Suites?) There are also hiking paths and the intriguing Mausoleum memorial to the McMillin family - their ashes are in the chairs around the table and there are multiple stories as to why one of the chairs has been demolished.Friday Harbor is more of a town with many more restaurants, book stores and boutiques. I could have spent at least an afternoon here but the family wasn't keen on shopping...
In addition to the towns, there are beautiful beaches with driftwood logs, foxes running amuck and more birds than I could count on the south side of the island. On the west side, you can see Canada and from Lime Kiln Point, we watched whales blowing their spouts right below where we were standing. The whale watching tours really aren't as humane as watching from the shore and I'm not so sure I would want to be in a little boat with pods of huge whales swimming by!
Finally, the highlight for me was the Pelindaba Lavender Farm. Imagine seeing acres and acres of bright purple fields in neat rows. The smell was heavenly.
This was a wonderful trip with younger children but would be great with older kids as well - especially if the family enjoys biking. While we opted to focus on this one island, it would easily combine with Orcas Island which has slightly better hiking and Victoria is only a quick commute away by ferry or flight.Please let me know if I can help you put together your own special trip in the Pacific Northwest!