I live in SF with my 9 year old daughter. Thinking about the stuff that makes her happy leads me to a potentially interesting idea for you, but it may not be for everyone. While Muir Woods are beautiful, they are painful on the weekends for all the reasons already mentioned. They will be packed even if you go with a tour. Would your family consider doing a hike instead?

To me me one of the joys of living here is the easy access to natural beauty. There are so many ways to experience it but the most accessible is going for a hike. If this sounds up your alley I’m happy to recommend some that will take your breath away and let you have a patch of redwoods just for yourself, either in Marin county or in big basin. This might require you to rent the car a day earlier but worth it in my opinion.

I agree with the comments re fisherman’s wharf. You will only be among tourists... i only go for one reason: it is a great way to see the sea lions. Instead consider a walk along Crissy Feild to the base of the GG bridge (start at Aquatic Park and walk west). You’re likely to see some sea lions frolicking in the waves and no Bubba Gumps to ruin the vibe. Or do the Lands end trail in the northwest corner of the city and walk all the way down to the beach.

Lastly my daughter loves the California Academy of Sciences in GG Park.

On edit, get up early and ride the cable cars. Kids will love it. You might as well.

Hope this helps