There is a great Alcatraz Island tour that leaves multiple times a day from Fisherman's Wharf. I recommend that you call ahead or book tickets online in advance because these tours fill up very fast. You usually have to book at least a day or two before you want to go (although that is less true in the off-season).
The boat takes you over to Alcatraz Island. It is a beautiful trip over and you can see the island and the Golden Gate Bridge in the background (if it is not too foggy). You can walk around the island and prison and stay for as long as you'd like--you don't have to go back on a specific boat.
I would recommend doing the guided audio tour of the prison. You just get a cassette that tells you where to go, the history of the prison, and some first-hand accounts from guards and inmates, but it makes it much more interesting. Its really neat to see and understand this piece of history.