Winona tore down it’s only downtown Hotel option to build the new bridge, which used to be the closet option, but you couldn’t dock there. There’s a Marina right across the bridge (Dick’s Marine) and the Winona Marina on the MN side a little further downstream. They might at least have an overnight slip for you and you can get a cab or uber to the hotels out on the highway. Great river town, went to college there! Great memories and did some really stupid things there but lived to tell the tale!
However you mentioned Trempealeau, and while smaller, I think it’s a cooler destination. Huge marina (Trempealeau Marina) there as well right above the Lock & Dam. Great restaurants – Sullivans, Historic Trempealeau Hotel, River Cafe. I know when my Dad went down the river years ago, Sullivans would send a car for you if you called from the Marina (it’s not really walking distance). One of the great small river towns.
Just call the Marinas and they’ll have info on how to access hotels, if they have shuttles, etc. The river sub-culture is such a cool vibe. I miss being down there a ton!