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.
We are in the South Bay now, have talked to Giorgio at Pete's Harbor, Ian at Bair Island, the Redwood City Harbor Master, Paul at Docktown and Mark at Westpoint. Only Docktown admitted to having slips for permanent live aboards. We were able to secure moorage only because we are bona fide transients. Westpoint is adding slips right now and, as a result will have a few more live aboard moorings available soon but this is a very expensive, brand new marina - first class in every way and worth the price IMO - but pricey. Mark Sanford, the Harbor Master is very choosy about whom he lets in and the rules are strict. Westpoint is the polar opposite of Docktown. More like a huge Yacht Club. When we tell people where we are moored they are astonished and usually ask how we got in here. Mark turns a lot of people away.
Docktown, on the other hand, has a certain...charm; if you do not mind the trailer park and the work-furlough program and sherrif's station next door; and of course having your keel in the mud except at high tide. I have to say, though, that the folks at Docktown seem a friendly bunch. They have their own, very egalitarian, yacht club and Paul, the Harbor Master seems a nice sort. When I spoke with him a few weeks ago they had LA slips available.