I wish I had more experience looking for luxury in Tokyo - I'm usually looking for "as cheap as I can tolerate". That said, a friend of mine that is definitely biased toward higher end places travels to Tokyo at least once or twice a year with his family, and has recommended the Azabujuban area the last couple of times I've been through, ascribing it the qualities that I think you're looking for. Grand Hyatt is not too far from there. This is all 2nd and 3rd hand, though. Everywhere in Tokyo is somewhat crowded.