You might consider Bayview State Park. It's near some of the smallest islands, easy kayak to Saddlebag, for example, and although the park isn't too exciting it gives you the access to the islands without the ferry trip or small sites. I assume you are familiar with the type of currents and tides in the San Juan Islands, though- if not, make sure you find out before kayaking there. The waters can be treacherous.
There is a state park on Orcas that has campsites that will take smaller RVs like Escapes. I've been tempted to try it but I haven't yet. Also, I think there is a commercial RV park or two on the west side of the island.