You can check in anytime day or night. In the morning, there may not be rooms available while the housekeeping staff completes their cleaning of the rooms. The hotel front desk is staffed 24 hours a day. Have fun--the hotel is very nice and be sure to take advantage of the free shuttle service (about every 20 minutes) to the subway and train stations.
Get an answer from Sheraton Miyako Hotel Tokyo staff and past guests.