Hog Island Oyster Co in the Ferry Building has a great clam chowder - expensive at $14 but is very generous with the seafood. My boyfriend who is originally from the East Coast claims it's the best clam chowder he's ever had.
Bar Crudo's clam chowder was also excellent, but it did have fish mixed in. I really enjoyed it though - I think it was the apple smoked bacon inside it! You probably need to secure reservations in advance.