Greeting from deep within the San Juan Islands !!!
Currently, I am "on the hook" in Blind Bay, on the North side of Shaw Island, just south of Orcas Island. It is my second time anchoring here, in a very protected little bay. I launched Blue Bayou in Bellingham on April 30, after a 900 mile ride from the California Delta, and we are.....doing the San Juan Islands. We have already been to Sidney, BC, and Victoria as well.
Spent last weekend in Anacortes (Cap Sante marina) with the C-Brats. You have to pay at least $50. there to launch with a sling, i.e. no ramp. There is a ramp about 4 miles west of Anacortes, at Washington Park, but very limited, and no place to leave your truck and trailer. With an R-25, truck and trailer, leaving the wheeled vehicles behind is THE paramont issue.
I researched this question pretty hard from California, and Bellingham offers free parking for your truck and trailer for a minimum of 5 days. I was able to get a month for free, just by asking for it. My pickup and trailer are sleeping in the Squalicum parking lot, and they have a signed permit in the windshield. The staff at Squalicum Harbor is excellent, and always helpful. Both Bellingham and Anacortes are just 1-2 hours from the inner San Juan Islands. I think they are the two best launching points, if you really want to do the San Juan Islands.
Bremerton is a whole other kettle of fish. Nowhere near the San Juan Islands. Unless you want to study the whole of Greater Puget Sound, I suggest either Bellingham or Anacortes.
As for going between the islands, they are all relatively close, and distances are not too far. Usually 1-3 hours will get you anywhere. The trick is to get to the right mooring for the night, and that's partly a matter of taste. Friday Harbor can't be beat, and is the County Seat, at the center. Get the chart books and Waggoner's, and also Ports and Passes (available at any Marine Supply store in Bellingham or Anacortes). It has all the tides and currents. Keep checking the weather reports for wind direction and speed.
Have a Safe Passage and a Great Time.