Trains are actually the thing you don’t need to worry about as they actually run more frequently over new years. (Though, long distance trains like the Shinkansen are often packed and impossible to book the few days before and after New Year’s.)

As for tourist sites and restaurants, be sure to do your research! They often close over the holidays.

I will!

Thank you Ohayo Travel for accepting my request

Sooo happy to hear from you as well Josh ! Definitely looking forward to strolling our first night around Shinjuku