Having recently been in SF, and living in LA, my two favorites (one from each) would be...

In LA, catch the Fenians out in Santa Ana at The Harp. They perform a mix of typical bar band covers (done fairly well) with a large rep of Irish folk and sea shanties. VERY fun.

In SF, Thursdays at Quinn's Lighthouse. Very fun evening of sea shanties and beer.

Of course, if you're around the first weekend of the month, I'd VERY strongly recommend the Hyde street Maritime museum on Saturday night. They do a group shanty sing in one of the various ships moored at the pier... it's an experience that needs to be had by any shanty fan.

That's my two and a half cents worth.

M