We go to both pretty regularly (not in the same day) here's my recommendation:
TLDR version: Dress kids up in Halloween costumes, park in the garage by children's museum, spend 9am-11:00am at the zoom. Bring cooler for drinks and PBJ and chips, ride the train walk to car to put away stroller and cooler. Then spend the rest of the afternoon in children's museum.
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Zoo opens at 9am and get there by 9:30. I recommend parking closer to the zoo. If you want to save money on parking, either in #1 or #2 on the map attached
https://imgur.com/a/4fgUPZ8If you park near the zoo, I recommend parking at #2 because it's easier to get out. It's a 1 mile walk from zoo to children's museum. You will not find any free parking near the museum.
I would pay for parking in the parking garage across the children's museum the walk to zoo and hit it up first. Zoo Boo is going on this weekend from 9-4 and your kids can dress up and they will have hand out candy and some activities. They should have little pumpkins that your kids can take with them.
You can bring a cooler to lug around for food and drinks. theres a restaurant by the rhinos that has hamburgers and pizza. Decent and Typical tourist price.
After the zoo, the train ride is nearby you can ride and you can point out to your kids the hobos around the importance of staying school in school. There's also a restaurant at the train station. Or there's bodegas taco shop about half a mile walk
Then walk back to your car so you stash your stroller and cooler. The museum also has trick or treating and some events in the afternoon.
If they are not tired enough after that, get patio table at Punk's in Rice Village And they can run around during dinner