Odaiba is well Odaiba.

But I wouldn't say Tokyo is crammed (other then usual) or extra crammed even with students off, especially this year when it falls on a Thursday, with the night preceding it and the day after all being normal business days.

Most people aren't off yet like New Years period to over rush and cram the trains, planes and automobiles.
That or my perspective is just off because I'm used to it here being crammed into a train every morning and evening and consider it "normal" when I run into a crowd and not much different, from any other day.

In the OP's case in what to watch out for, well Tokyo there will always be crowds depending on where you go no matter what time of year.
For Christmas again it falls on normal business days to, so many places will be open like usual (vs. closed New Years time). So you can expect things to operate as usual, no modified train scheduling, closures or early closures.

My friends don't believe me when I tell them about the lines outside Krispy Kreme on a Regular day.