I would recommend the Grand Hyatt on Union Square or the Hyatt at Fisherman's Wharf. Grand Hyatt for it's amazing views and close proximitiy to shopping and Fisherman's Wharf for it's recently renovated rooms (32" LCD TV's in all rooms) and fitness center as well as being close to all tours such as Alcatraz etc. Fisherman's Wharf has limited views compared to the other two, but has the best rooms.