When it comes to eating kosher in the Bay Area in general, choices are pretty limited.
If you find yourself in San Francisco, there are currently 2 choices downtown:
The S.F. - New York Deli is a walk-up location right in Embarcadero Center. There is a lot to do in the area, so it's very convenient if you're visiting from out of town. The service is quick and the food is very tasty. A little on the pricy side, but there's nothing unusual about that in San Francisco.
Less than a mile away, you'll find the Sabra Grill, which has a typical Israeli restaurant menu. If you're looking for a sitdown meal in San Francisco, this is the one and only place. The prices are on the high side, even for Bay area standards, but there is no doubt of the convenience of the location.