I live a couple hours from St. Louis and definitely agree with hitting the Zoo, the arch, Science Center, Magic House, Botanical Gardens, Grant's Farm...all great possibilities.
I'm going to be the odd duck out and say, while the City Museum is incredibly cool with some very neat and unusual things, I'm not the world's biggest fan. My son always has fun there. But it's an acquired taste and I think it's better to less nervous parents than myself or something. I'm not bothered by most of the stuff but it is very, VERY easy to lose a child there. Tunnels and slides and pathways that start in one place, or in some cases on one floor, and end up in an entirely different place. (Again, or floor.) My son got lost there the last time we were there and it was really upsetting to him. There's just so much stuff everywhere and, purposefully, none of it makes a lot of sense. Which meant when he came out on the other side of a tunnel he climbed through, he couldn't find his way back to me. And I couldn't find him at all. It was very scary. I'm not saying don't go. Just be mindful if you do.
Not sure how old your DS was, but we have never had any problems at the City Museum. When the kids were pre-schoolers, 4 and under we each followed one through the tunnels and wherever they went. We had so much fun exploring with them. By the time they reached 5 they were too fast for us! We just said we were going to stay in a certain area (the outside, the roof, the enchanted caves, the main 1st floor area) and let the kids run and play as much as they wanted in that particular area. We'd see them here and there, every few minutes. Eventually they come find us and are ready to move to the next area. The museum is divided into very separate areas that make this very easy to do! Don't worry about trying to see them every moment, just make sure you all play in the same area of the museum and everyone knows not to leave that area. Now that the kids are 9 & 10, they are given a bit more freedom. We go with a group of friends and I may be outside with DS and his buddies and let DD and her friends go on to the 3rd floor knowing they have to report back to me if they decide to go anywhere else. It is an amazing place, not to be missed!!