There are mostly the basic, international chains: Holiday Inn, Mariott, Sheraton, etc. This one has a 24 hour shuttle to the airport: http://doubletree1.hilton.com/en_US/dt/ ... a/index.do
which will be helpful if you want to explore the city a little bit that afternoon, because you can BART in.
I think it makes sense to stay at an airport hotel because that will give you door-to-door service and you won't have to carry your luggage very far and you'll be able to sleep in a bit more. I would just look for one that has regular shuttle services, so once you check in, you can take the shuttle back to the airport and then take BART into SF.