Latitude 38 is the best place to start. There are fewer and fewer livaboard marinas in the bay, and with the housing prices the way they are a lot of demand. Sausalito used to have quite a few, but many were cleared out.
Call Around - in the South Bay Redwood City have a limited number of slips available, as does Pete's Harbor. Most of the harbor masters seem to have time to chat, and may give you some ideas.