I've been doing a lot of investigation over the last 6+ months on where I want to live-aboard in the bay area and I have settled on West Point Harbor in Redwood City. It has excellent weather
, it's close to 101 which gives you easy access to SF and SF International Airport
without having to pay road tolls as well as giving you quick access to the South Bay. The harbor master is extremely aggressive towards anyone who is not a member
that shows up on marina property, this makes it safer than any other marina I have visited in the bay and makes leaving the boat for an extended period of time a safer feeling. It's not maxed out in occupancy and they have very nice facilities(it's a fairly new marina).
The only draw-back is that you're further south of the best sailing in the bay and that adds some time to your weekend sailing excursions.