Hmmm, I have stayed at the Fairmont. It's very nice but if you take a car the parking is insanely expensive. In 2007 it was $52/day! I'm going this week but will be staying in Vallejo and taking the ferry to the city, then spending the night on Alcatraz. Don't think those are the accommodations you are looking for. LOL!
What's your budget? That might help with suggestions!