I've been to San Francisco several times and it's great.
Hotels can be hit and miss with a lot of bad ones mixed in.... but I highly recommend this one I just stayed at called the SW Hotel. It's in North Beach right by the famous City Lights Book store and is walking distance (or trolly) to the Warf.
http://www.swhotel.com/
I recommend it because it was really nice for the price and the location is great.
Alcatraz:
I'd get tickets right away. They can book right up in the summer. Better safe than sorry.
I really liked the night tour. The Hospital ward was open and there was a freer atmosphere conducive to wandering unsupervised. It is a lot scarier at night too which suits the vibe.
Here's some Alcatraz photos I took with my crappy point and shoot:
Have fun and bring a better camera than I did. =)