DO NOT stay at the US Grant, it is a total piece of s**t hotel, way over priced for what it is.
As HG say the Del Coronado is nice, also on the list of nice hotels I have stayed at in San Diego
The Omni
The Marriot Gaslamp
The W
The Manchester Grand Hyatt
Out of those I would probably say the Omni gets my vote, with the Manchester Grand a close second.
One thing to note, if you have a car, the parking costs at these hotels makes SFO look like a bargin, off the top of my head all of the above charge $20+ a night for self parking and $40+ for valet parking.