Hi
I've been to Alcatraz when I've been to SF recently (nothing to do with JY). I booked the tour in advance from the UK, and it really is very straightforward.
I would echo everything that Ben says. It's a must do tour and is relatively inexpensive, the "cruise" out is enjoyable as well. The Alcatraz tours can get very, very busy, and I would strongly suggest that you book it in advance. If you leave it until you actually get to SF, then I suspect that you would have a very limited choice of times, and it may even be that the tour is fully booked for the next couple of days.
I've noticed that people on this holiday have posted on this site, and thereby got a number of people on a particular holiday all to all book on the same Alcatraz tour, and this is a possibility especially as you've got a few months before your holiday.
Enjoy SF.
Stuart