Some ideas that my kids always enjoy. Some have already been mentioned.
Rent bikes and bike along waterfront
Go the Wave Organ. It's an interesting art piece in the Marina District neighborhood. If you go, go at around high tide. Also has great views of the bay and the Golden Gate bridge.
Go to Chinatown and walk on Stockton St. Stop in the fruit/veggie markets, fish markets, get some snacks. Taking the 30 bus to get there is very interesting. Grant St has the souvenir shops while Stockton St is where people go to shop.
Go on a SF CityGuide walking tour. Lots of different topics and they have good guides. Free with a donation.
Go to the Farmer's Market on Saturday morning at the Ferry Building. Go around the back to the food stands, get some breakfast/lunch and enjoy a great view of the Bay Bridge while eating
Musee Mechanique - cool old arcade games from the 1920's to 90's.
Cable Car Museum - a fun stop to see how it all works
If your kid needs to blow off steam, there's a nice playground close by the Ferry Building (Sue Bierman Park).
There's a fun playground in the Yerba Buena park - https://yerbabuenagardens.com/childrens-playground-like-no-other-in-sf/
Coit Tower is okay - it has a good view but once you are done with that, there's not much else there.
Exploratorium - Science based kid museum. Tons of hands on kid activities