I used to live in the South Bay so I've got a couple of suggestions depending on how far you're willing to drive.
Check out the area around Palo Alto Airport and the Ravenswood Open Space Preserve. I've gone there a number of times at night when the tides are favorable and it's the best mud I've found. The only downside is you have to walk a ways from wherever you park and the neighborhood is a bit sketchy.
Also, because of the drought, a lot of the local reservoirs are very low and the muddy bottoms are exposed. I went to Lexington Reservoir while visiting back in July and it was quite fun, but Calero, Chesbro, and Uvas are all pretty dry and exposed right now. If I was in the area again, I'd be very tempted to go check them out!
I'm not sure how other's find spots but I generally scope out places with Google Maps or Google Earth. That being said, I think there are some potentially good spots not too far from SF. Check out the shoreline east of 101 in Corte Madera. Also, look around the areas off highway 37 between Novato and Vallejo. It's fairly remote and there are lots and lots of tidal flats for getting dirty and channels for getting cleaned up afterward.