Steve picked two of the best, here's a little more info
Treasure Island, aka Clipper Cove, is beautiful and, with a little imagination, the traffic noise (which really isn't that bad) sounds a bit like surf. At sunset, the windows in the buildings in the East Bay (Oakland & Berkeley) look like they're on fire. Don't anchor too close to the old Navy docks on the north side on your way in, I hear there are sunken cables and other junk to foul your anchor. By the way, Clipper Cove is named after the Pan American Clippers that were based there and flew to the far east, not clipper ships. Hospital Cove at Angel Island is especially nice during the week. During the uncrowded midweek, you can tie up to just one mooring bouy and swing as if at anchor. During weekends, you need to tie up bow and stern which can be a bit of a challenge with other boats tied to the same bouys. The docks are day-use only. We had an unexpected treat here one night when the seawater luminesed (sp?) as it swirled in the head when we flushed in the dark. It was like aquatic fireworks (I amuse easily). Another spot is the anchorage at Aquatic Park near the Maritime Museum. The catch here is that you're not supposed to use your motor but manuever under sail only due to the swimmers in the water. It's well protected so it's not all that difficult.
