San Juans in a small boat is very do-able. I don't do much camping so can't help much there. Sucia, Jones, Stuart, etc. are state parks and have places to pitch a tent.
Roche Harbor, Deer Harbor, Fisherman Bay, Rosario, all have hotels associated with or very near the docks.
Friday Harbor has places to stay further up the hill in town but nothing close to the harbor. There used to be a B&B boat in the port but I don't think it is still operating.