I've done charters with both San Juan Sailing and Anacortes Yacht Charters. Both are good. SJS has more sailboats and the boats are more consistently equipped with their required gear. Anacortes is closer to the San Juans, but it's not a major factor to me.
You'll want the Waggoner's Guide, as mentioned already. Also, currents are strong so you'll want to get a tide atlas and try to be going with the current rather than against. Make a huge difference.
You'll want the Waggoner's Guide, as mentioned already. Also, currents are strong so you'll want to get a tide atlas and try to be going with the current rather than against. Make a huge difference.