About 1.5 hours south is Muir Woods. We were there when my oldest was about a year old and she loved hiking through the trails and checking out the huge trees. You can also venture into San Francisco. The Sea Lions at Pier 39 are really cool and there's lots in that area that will be interesting to kids.
I would do Armstrong woods over Muir with a toddler. It's much more accessible from St. Helena and is a very similar view, with much fewer tourists.
I second the children's museum in Santa Rosa, my good friend is a manager and we have spent lots of time there. I didn't catch how old, but there's the Charles Schultz museum and ice rink right next door as well.
It's a little pricy, but Safari West is an awesome tour in between St. Helena and Santa Rosa. (Be aware that this is where the fires were and it's a little eerie driving through).
Also PM me, but I have a toddler/preschooler and grew up in Napa and lived in Sonoma County for over a decade.