Where is the best place to get a haul-out/bottom-job in the SF Bay area??

Maybe I'm partial to KKMI because they are close to my Brickyard Cove Marina, I can drop off the boat, walk back to the Marina and get my car.

Yes, they are known for the monster boats and huge wallets that support them. But if you establish a relationship with them, show your knowledge, stay on top of things, they work out very well, won't rip you off.
I've had two boats pulled there, bottom jobs plus some extras, made it really clear I'm on a budget, they were fine - and where else do you get a bottle of wine when you pay your bill???

We never had Berkeley Marine do any work on our boat, but we did use the yard last year and they are a nice place for DIY.