Clipper Cove by the Bay Bridge offers the very good protection. It's good for a few days. Needs a permit
from Treasure Island, available online.
Mcnears beach/ China Camp, located on the west side of San Pablo Bay, is a nice quiet Anchorage. Free, No permit
required. It can get a little choppy in the afternoon, but not too bad. Avoid if winds from North or east.
Paradise Cove is not too bad on the east side of Tiburon. The ferry
wakes are a problem there though. Free.
Aquatic Park is okay, you have to watch out for all the swimmers in the water
when entering it. You also feel like you're in a fishbowl with all the people walking on the Pier. I think there's a fee for that now too.
Richardson Bay near cone Rock, that is away from the anchor outs, it's quite pleasant as well. Free.
Argyll Cove at Angel Island has mooring
balls where you can stay at overnight. They also have daytime Docks. Both require Fee.