Don't know what sort of things you are into, but (IMO) Alcatraz is waaaaay over-rated. If you guys like walking, hiking, or casual biking, you might like a trip to Angel Island more; it's the island next to Alcatraz.
Angel Island is about twice the size of Alcatraz. It was never a prison, so you don't get that "this used to be a prison" experience, but it's a great place for picnics, has bike rentals, and offers sweeping views of the whole Bay Area, including three bridges (Golden Gate, Bay, and Richmond-San Rafael). With the great weather we've had this week, I imagine the views will be fantastic. The island has a fairly level perimeter road that's ~5 miles in circumference and very good for biking or walking. It also has some foot trails, including a trail to the top of Mt. Livermore (the island's peak) that, at 700+ feet, also offers incredible views of the Bay Area. There's a small cafe on the island, or you can bring a lunch. Only way on or off is via ferry, which leaves from Pier 41 (next to Pier 39, same ferry port as the ferry to Alcatraz). We spent Labor Day there with our kids and some friends and had a great time.
Also, another recommendation for the Exploratorium -- always a good time.