City Museum is a hundred-year-old warehouse in downtown St. Louis in which artists have repurposed the pieces of old cities to build miles of tunnels, slides, climbers, bridges, and castles. There are secret passages and grand galleries. Playgrounds and ball pits. A circus and a train. A rooftop school bus and a Ferris wheel.
This is a great place for kids young and old.
I would encourage all who have not been to the A-B Brewery in St. Louis to try and make it a priority while in town. While it could be argued to be a bit "commercial", it's still iconic. If you are travelling with children, there is a Clydesdale tour that is family friendly.
The St. Louis Zoo is FREE and one of the best in the US. It's also inside the largest park in St. Louis, Forest Park.
The aquarium is part of the newly renovated Union Station in downtown St. Louis (built by McCarthy ;)). There are several other attractions in Union Station including the St. Louis Ferris wheel, mini golf and a Halloween Train or Treat.