If he has any interest in nature or hiking, Muir Woods (one of the places with tall redwoods) is a relatively short drive across the Golden Gate bridge. We went on a weekday morning right when the park opened, and managed to go over an hour without seeing another human.
The Walt Disney museum is surprisingly good as well. Though it runs as an actual museum rather than a kid's playpen.
Three days likely makes it too short (as you could spend the time in SF easily), but it is also only about an hour to San Jose, so if the Sharks are playing, you can consider a hockey game. The other San Jose places of interest I have hit up probably wouldn't appeal to a nine year old -- the Computer History Museum and Winchester House.
Last edited by Resolute 14; 01-31-2017 at 11:24 AM.
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