The camping itself is quite similar between islands; so the "best" place to camp in the San Juan Islands would probably depend on what other attractions and activities you were interested in. Each island has its own unique personality. Do you plan on bringing your car to the islands? What kinds of things are you interested in seeing? I am contacting
West beach resort and
Lakedale Resort to see if they would like to contribute to the conversation. How many days are you planning on staying in the islands?