I live in the Peninsula so I've only been to two stores in SF: ImagiKnit and Greenwich Yarn.
ImagiKnit (Castro area) was my favorite. Huge selection and reasonable prices. Since I went when they were having a sale, their prices were great! Oh, and did I mention: they have plenty of mmmmalabrigo.
The one con, according to a friend, is that apparently they have an employee who is flat-out rude. Luckily, I didn't encounter this person and my experience there was quite enjoyable!
Greenwich Yarn (Marina area) is -- I think, don't hold me to this -- the oldest yarn shop in San Francisco. They've been open for about 30 years! The store is pretty small and their selection is a little limited, compared to ImagiKnit's, but the owner, Laurie, was a sweetheart! Interestingly enough, when my friend (same one as above) went she found Laurie to be a rather cold and aloof. Hmmm, maybe my friend brings out the worst in people?
Anyhow, hope that helps. Have a wonderful time visiting California and if possible, try to visit a vineyard or two. We have the best Cabernet Sauvignons in the world -- a little Cali pride here