Did this last year. Slept on the plane, used the showers at Haneda, and took the limo bus to Hilton Tokyo. Was expecting just to drop bags with bellhop and come back that afternoon. Hah! Staff insisted on checking in, upgraded to Exec room then, was apologized to because the room wasn't ready yet and invited to use the fitness center if I'd like to shower and change and the Exec Lounge for breakfast.

Do you have any status with Hilton? Regardless, I'd just contact the hotel and see about arranging an early check in so it's settled prior to arrival. There always seems to be a number of early morning arrivals there when I've stayed since.