I used to live in San Francisco and used to work at Grant's. Haven't been there for a couple of years since moving down to San Diego, but they had a few chairs out in their smoking lounge and a pretty decent sized humidor. When I worked there, we weren't allowed to smoke until after 5 pm due to the neighbors complaining.
I absolutely love The Occidental. It's a great cigar bar, though a little small. However, it's a fully stocked bar. They have cigars there, but you are better off buying at Grant's then heading over there because their cigar prices are a little high. Grant's is only about 5 blocks away from them.
Cigar Bar and Grill is fine, though I rarely went there. They have food, drinks, and sometimes live music, but you can't smoke inside.
Telford's in Mill Valley is fine, but you have to pay to stay or spend at least $25. Pretty easy to do with California prices. Knickerbockers is cool too. Never been to Cigar Loft or Casa Belicoso, but I have heard good things.
Hope this helps.