We have holidayed in Japan in Dec/Jan for 3 of the past 4 years. I think it's a great time to go as it's not too hot and not too rainy. You are there for sumo season, too.

I agree that a side trip to Kyoto is worthwhile and that you should take a Nozomi Shinkansen. Maybe 2 nts in Kyoto and 5 in Tokyo, although with all the great food and shopping, we find 2 weeks is too short in Japan.

Have a great trip.