I understand that, the "I live here so I never do the touristy stuff" curse. Happens to my wife and I all the time, we will go see the Boston sights only when family or friends are visiting but not by ourselves.

We enjoyed the Alcatraz tour. A short boat ride, an intro film, some time wandering around the island, and then an interesting self-guided self-paced audio tour of the cellhouse. Great views of the city and Golden Gate, too.

A good afternoon's worth as long as the weather is cooperative. (If it's rainy you probably wouldn't want to spend time wandering the island.)