I left my suitcase for 1 night in Kusatsu while travelling in Tokyo.
Most places that allow long-term storage of suitcases open at 10am, but this place only opens at 8am. It rained a lot on the day of departure, so there was a lot of rainwater splashing on my suitcase, but they wiped it carefully and took it to the storage area.
If you are travelling to Ueno early in the morning by shinkansen and have a short trip to other areas, this is the place to leave your luggage.