Hope we can touch tips when you are out here! We will be moving from the SF around then though.
Open to AirBnb? On their search criteria or when looking at results there is family friendly listings. We lived in the Marina/Cow Hollow area for a while. It is nice with access to killer playgrounds and walking spots. Otherwise, Fisherman's Wharf area is preferable due to proximity of hotels and kid stuff nearby. Grab the historic F car MUNI lines. They are the slow ones that lumber up and down the Embarcadero and fun to ride.
One of our favorite spots is the California Academy of Sciences. They have an aquarium and many interactive exhibits for kids.
https://www.calacademy.org
Across the way is the De Young Museum. There is a free observation tour where you can see the entire City and many parts of the bay.
We did this exact trip above a few weeks ago. I have a membership to the Cal Academy and free passes if you want to meet up. We could even brown bag some beers in the park
Shoot me a PM and I can give you some more detailed help.