I have gone on the Alcatraz Tour twice now, both times utilizing Pier 39's Blue and Gold Fleet. Both times I was very impressed with the boat quality, and enjoyed the quick ride out to the rocky and dangerous island. Once you arrive on the island, you are greeted by a cheery and informative ranger, who speaks to the group for a few moments. You are then guided up the large hill (take a big breath everyone!) and to the beginnings of the building structures.
You are able to view previous quarters of the guards, along with the rubble of some quarters that had caught fire. You eventually reach the actual prison, which is in quite nice condition on the inside. You are given headsets to wear and guide you through the prison house. This is very nice and convenient. It allows you to take as much time as you'd like in the prison. There are boats that head back to the city every 30 minutes or so, so you may take as much time as you'd like on the island. It is a great photo opportunity of the city!
Also, if you go during the winter months, you are allowed on the fenced path around the edge of the island (during other months, there is bird migration in those areas, so they prohibit it). I have also heard that their evening tour is superb. Apparently, they take you into other areas of the prison, that the day tours do not go into. I will be doing that tour on my next stop!