The IC on Howard St. is probably your best bet. I don't like the location of the Mark Hopkins, and depending on your status (and if they are in a good mood if you are only PC elite), you may get a nice room or you might get another room - this hotel is "venerable" which can mean ... well... luxury, or a closet.
The Holiday Inns - 8th& Market - seedy location but convenient for transport. Van Ness - inconvenient. Are there others? Wharf? Forget it.