Holiday Inn Express & Suites Winona (8.6/10 from 173 reviews), AmericInn by Wyndham Winona (8.2/10 from 136 reviews), and Fairfield Inn & Suites by Marriott Winona (9.2/10 from 92 reviews) are all highly rated places to stay in Winona.
Alexander Mansion Bed And Breakfast is a good hotel close to Winona Amtrak Station - it has scored 9.7 over 102 reviews from HotelsCombined users.