This is as good a place as any to do a roundup of Tokyo hotels using my unpatented, not very helpful ratings system:

Park Hyatt: (9) Room-7, Facilities-9, Service-10, Wow-7 (views, interior design)
New Four Seasons (near train station) (7) Room-6, Facilities-6, Service-10, Wow-3 (the only real boutique hotel in Tokyo)
Grand Hyatt: (6) Room-6, Facilities-6, Service-6, Wow-0
Old Four Seasons: (5), Room-5, Facilities-5, Service-7, Wow-2 (Huge grounds, including a temple, a crazy luxury considering Tokyo land prices)
Westin: (4) Room-4, Facilities-4, Service-6, Wow-0
Century Hyatt (3), Room-4, Facilities-3, Service-4, Wow-0
Imperial (2), Room-2, Facilities-2, Service-6, wow-0

There's also a newish Mandarin Oriental that I've never stayed at but I hear is in the same league as the Park Hyatt