In no particular order:
Train Town (reminds me of Mini City in Durban)
Bay Area Discovery Museum‘s “tot spot” in Sausalito. The first Wednesday of every month is free.
Cartoon Art Museum Tuesdays are pay-what-you-wish.
Children’s Park in Golden Gate Park
Dennis the Menace Park in Monterrey
When the baby is a little older, I’d love to visit San Francisco’s Center for the Book.