Hello
We will be in Tokyo Dec 29-Jan 3, tickets and hotel (Ginza) already booked. I can't seem to find reliable information on how much of Tokyo will be closed during the holidays. The hotel is warning me that Tokyo will be much more quite and most restaurants, bars, stores, museums, markets, etc.. are all closed Dec 30-Jan 3. But then other websites say mom and pop shops yes likely to be closed, but most of everything in the center areas will be running and that I shouldn't worry. Can anyone provide any guidance? Also, any suggestions of what to do on New Years Eve?

Thanks so so much!

Got to take the Ginza hotel's advice (warning) at least as far as it applies to Ginza area. It will be slow but you won't go hungry and might not get bored.

I would trust this:
Visiting Japan during New Year (japan-guide.com)
Ask at flyertalk.

Maybe Timeout Tokyo has info about open/closed days. You just might want to plan more.

Over New Years the Ginza area will be packed with shoppers. During New Years major luxury retailers and department stores offer fukubukuro or lucky bags for sale. These are grab bags filled with random items costing much less than regular prices. Shoppers line up to get in on these sales hoping for something good, hence the name lucky bag.