I suspect you can get a decent bowl of New England Clam chowder at the Blue Mermaid Chowderhouse and Bar across from the National Maritime Museum at the Hyde Street Pier.

I can't say for sure, because *I* ordered the Mussel and Sausage Chowder....which was excellent, if a bit pricey...

I would observe that lots more places in SFO serve Manhattan Chowder than New England, because of the prevalence of Italian/Portuguese influences from the early fishing fleet on the waterfront. Traditional SFO chowders tend to have a bit more of a minestrone style than a Boston/cream base.

Of course, the best Clam Chowder in California is not in SFO, but 175 miles of driving North to Noyo Harbor (just South of Fort Bragg), where you will find Carine's Fish Grotto, which looks like a dive or a fisherman's bar, but is actually a family restaurant where mama's cooking what her husband and sons catch on the boat tied up out back. Big portions of the amazing chowder and seafood and home-style Italian specialties.