In the historic district of St. Charles, right on the river. The historic district is full of fun shops and places to eat. If you go the 3rd weekend in May you can see the Lewis and Clark Heritage Festival as well.
The Lewis and Clark Boathouse is a great place to stop as part of a trip to historic St. Charles. With educational information and exhibits regarding Lewis and Clark, Native American this small museum is not geared for younger children. The admission fee is reasonable and the museum is located next to great shops and restaurants on Main Street, St. Charles.
This museum is worth the stop nestled in the historic district of St. Charles on the river. The museum is self guided (which I find more child friendly). It has displays from the Lewis and Clark expedition, Native American displays and the Missouri River's ecosystem. We enjoyed the displays and overall feel of the museum. It is on the smaller size, so its great for shorter attention spans and can easily be folded in to other things to see around town or makes a great place to stop for an activity and picnic on the river.
They have gift shop. There are tons of cafes and restaurants nearby for lunch (within walking disance) and there is plent of parking.