Shangri-la Tokyo held my bags for 2 days while I was in Kyoto. Depends on the hotel I guess. If you are staying long enough you can TaQ-bin them there, but do it 24 hours in advance.
Also on the Shinkansen, you can reserve a few days ahead of your trip at any Shinkansen Ticket Office for seats at the back of the car so you can put your luggage there, if not it can always go in front of you (most people dont recline their seats when there's someone behind them). The overhead also fits small suit cases.