I second the Alcatraz night tour- not only is it a much cooler way to experience Alcatraz, you also get stunning views of both SF and the bridge. I really love your list, even though I don't know what the Exploratorium is.
Interesting fact about it that I only recently found out:
The Exploratorium was founded by Robert Oppenheimer[1] ("the father of the atomic bomb") after his forced resignation.[2] If you keep an eye out, there are some plaques talking about this history at the museum, and there's also at least one uncaptioned atomic-bomb-related photo (of the first milliseconds of an atomic bomb explosion) on the walls.