We did 3 days in SF 2 years ago with our son, who was 9 at the time. He has ADHD but it was undiagnosed at the time.
He loved Chinatown, although my DH & I could have done with a little less Chinatown. We were staying near there, so we'd walk through it each day.
He also really loved Alcatraz, but he has a fascination with both history and prison. Alcatraz is a great tour, even at age 9.
One day, we rented bikes and biked over the Golden Gate Bridge to Sausalito, although that was a bit of a mental challenge. We took the ferry back. He really liked both Sausalito and the ferry ride. (He liked the GGB bike, but was having a bit of a meltdown over random stuff.) We also went to Ghirardelli Square after the ride and got some needed sweets.
FYI, on our first morning in SF, we woke up on Eastern Time and just decided to start the day since no one was able to sleep any longer. We went to the Wharf early and watched the sea lions. It was nice because there wasn't a large crowd and he could run around and burn off some energy. From there, we walked to Lombard Street, Coit Tower, and the Telegraph Hills steps. Maybe something else. We headed over to Tony's Pizza in Little Italy (Stockton Street). There was a great playground right by the restaurant and he ran around more there. From there, we walked to Giants Stadium and watched a baseball game from the outfield peepholes and looked into McCovey Cove at all the kayaks and boats. We are a baseball family, so it was fun telling him about Barry Bonds (except for the steroids part).