As far as rates at a lot of the hotels in Tokyo, Xmas Eve (especially when it falls on a Fri or Sat) and the last few nights in Dec (when everyone's holiday) are definitely much more expensive. This applies to pretty much all city hotels and luxury hotels in prime areas of Tokyo/Yokohama like Marunouchi, Shinjuku, Shibuya, Odaiba and Minatomirai.

On the other hand, rates on those dates tend to be not much different than any other dates when you're talking about outer locations like Tachikawa.