here's three
The closest to you would be Sams in Tiberon. The Ramp in SF and Quinn's Lighthouse in Oakland are also supposed to be good. Honestly, I've only sailed into Sams once for brunch, but friends have sworn by the Ramp, and I have eaten several times at Quinns where they have a dock, but i'm not sure how it's used. You can also park at South Beach for a reasonable time (3 hours?) at the guest dock and there are several restaurants nearby.
Don Wigle
Wiggle Room
E 38 #8