Just to warn you now, depending on where you are from, Tokyo in January is COLD! I've been to Japan in January and February and while I've enjoyed my trips it seemed really cold and yes, I am from the NorthEast so I should be used to the cold, but I guess because I was outside touring so much it was harder.
Christmas itself is not a holiday in Japan, but New Years is and there are a lot of holidays in late December around New Years and post New Years making it an expensive and crowded time. I also personally find New Years really hard as a tourist because so many things close for 3-4 days. I've only been to Japan once for New Years, and I'm not willing to go back unless I am actually living there.
I went to Tokyo DisneySea once in '09 in October. It was insanely crowded. Everything had 2+ hour lines and I was pretty miserable. It's a beautiful park, but I'd rather be out being touristy than paying money to walk around a theme park. I go to a theme park for rides and attractions, not to admire the scenery. Yes, while doing my rides and attractions I love a good atmosphere, but that is not enough on its own.
We are going to try Tokyo Disney again in June. All the crowd calendar sites claim it should not be so bad for our dates. I'm planning to stay on property so we can park hop because I know we can't make a day of DisneySea because my daughter is under 117 cm which means: Indiana Jones, Raging Spirits, and Journey to the Center of the Earth are no goes. She didn't enjoy WDW!Tower of Terror so that is also a no go.
We went to Tokyo for 10 days last June post school. I think we paid about 2k for airfare (like a previous poster I only want direct flights, and I specifically wanted JAL or ANA. I prefer Japanese airlines), another $400 for rail passes, maybe $100 for other train/subway/bus trips. (At the time my daughter was under 6 so she was free on public transportation. However I did buy her a rail pass, so we could reserve seats on the shinkansen. I was not going to have her sit on my lap for 2+ hours!) I splurged $450 for 1 night at the Tokyo Station Hotel, which is amazing and might have rooms for a family of 6, but it will cost you a lot. (I would also check other luxury hotels or ryokans since they are more likely to have rooms that fit more people.) We then spent a little under $400 for 2 nights in Hakone. $574 for 4 nights in Kyoto, $250 for 1 night special package for Osaka Universal, and about $500 for 3 more nights in Tokyo for a grand total of: 2174. The Tokyo Station was the only hotel I stayed on par with the Poly. So 4674, plus meals, activities outside of Universal, and lots of souvenirs. This was for 1 adult and 1 child at the end of June. I find WDW is cheaper, but we are DVC owners and I never do a meal plan because it's so not worth it for how we eat. We usually stay at the Poly or VGF. Hope this helps!