I live about 40 minutes away from SF and would definitely recommend the Alcatraz tour. Getting them in advance is hit or miss. There are times when they are booked for weeks and then there are times where you can get them 1-2 days in advance. I would call ahead and ask (but would probably get them ahead of time).
Check out a Giants game as well (try and make it a night game as the atmosphere is amazing). Save some time for Chinatown as well on top of all the other touristy stuff (Fisherman's Wharf, Golden Gate Bridge, etc).
In terms of the hotel, no idea as I live 40 minutes away so either I drive back or stay with friends in the city.
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