If you want a luxury hotel with convenient access to the Shinkansen (which takes you to Kyoto) I would suggest the Four Seasons Marunouchi. It is immediately next to Tokyo Station.

Park Hyatt and Grand Hyatt are great hotels, but they are not conveniently located for a whistle stop NRT-Kyoto-NRT run.

Since you've decided to come another time, I'd be inclined to skip Kyoto this time.