LaCrosse is a good starting place. I think hp500 puts in there also when he come to the river.
If you head north, Treasure Island Casino in Red Wing would be a good destination. It would be a full day of boating with a distance of around 100 miles and 6 locks to go through. There are a few other places, but no hotels with a dock. There are plenty of marinas that will shuttle you to a nearby one. In Lacrosse, there is a hotel on the Black River.
Our marina (Great River Harbor in Alma) has a couple of A-Frames that you can rent out. We could hook up on your way up from Lacrosse and show you the local watering holes on the river.
If you head south, there is Lansing, Marquette and Prarie du Chien, and even Dubuque.