Trains/hotels during holidays

How will trains and hotels be affected during the holidays? I'm able to go on a spur of the moment trip to Japan, I'll be going from December 15th to January 15th, I was wondering how bad trains will be affected a few days before and after Christmas/ new years.

I'll be in Tokyo 16th-23rd, I plan to go to Hakone on the 23rd until the 27th, then go to Kyoto until the 3rd. I'm still figuring out what I'm doing for the last chunk of my stay.

my time will be mostly open while I'm in the big cities, so do you suggest I get a 21 day Japan rail pass? Think it'll be worth it?

I was wondering how bad trains will be affected a few days before and after Christmas/ new years.

http://www.japan-guide.com/e/e2276.html

I'll be in Tokyo 16th-23rd,

If you don't have any major side trips then you don't need an active JR Pass during this time.

I plan to go to Hakone on the 23rd until the 27th,

That is very long for Hakone. Again, you don't need a JR Pass during this time.

then go to Kyoto until the 3rd. I'm still figuring out what I'm doing for the last chunk of my stay.

my time will be mostly open while I'm in the big cities, so do you suggest I get a 21 day Japan rail pass? Think it'll be worth it?

Depends where you plan on going of course. What airport do you depart from? In general I'd activate a JR Pass when you leave Hakone for Kyoto and use it to move around from there. You could let it expire once you get back to Tokyo.

Enjoy your trip!