Be sure to stop in Dubuque, Iowa for the Mississippi River Museum & Aquarium plus the Fenelon Place elevator for the views!
Historic Nauvoo, IL with the Mormon Temple plus across the BNSF Railroad/Swingspan Bridge to Fort Madison, Iowa is a replica of Old Fort Madison to tour right in Riverview Park.
If you are going to be going to Hannibal, and have not ever been to St Louis, I would go another 2 hours to see the river there with the Arch, etc.
McGregor, Iowa is an interesting little town. Worth an hour or so for the little shops. La Crosse is also nice. There's the Effigy Mounds National Monument which, if anything, provides excellent views of the Mississippi and preserves what that part of the prairie once looked like. Then there's the Red Wing shoe museum in Red Wing, Minnesota: www.redwing.org/red-wing-shoe-store-museum/. And I don't believe it's open for tours, but I've always been interested in the Keokuk Dam: http://www.keokukiowatourism.org/lock.htm
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