December 29 - 5 was too closed to new year countdown that why Hotel at Tokyo price will be triple.
Winter or Summer....70% shop will be closed at 8pm......most late will be 10pm
After 10pm only left Izakaya

Winter it gets dark early, and take note that on NY eve a lot of places will be closed. Friends and I went to Takashimaya on NY Eve around 5pm and everything in the food section of the store was selling fast (cakes, noodles, bentou etc). Go to temple on New Year's morning. Yes there'll be huge crowd but it's also interesting to observe the Japanese celebration.

On 2nd January, get your money ready for fukubukuro (福袋) as you'll splurge on shopping. 福袋 only happens on 2nd January and you'll see a lot of great promotion, offers and attractive sales. For major brands like Starbucks, Apple etc they usually sell the 福袋 tickets 6 months ahead (or they draw lots, whichever way) so it's hard to get the 福袋 from these stores.

SIM Card - consider getting it here instead of in Tokyo.
I recommend this: https://hello1010.my/country/asia/japan.html

From google you easily find where is Tokyo firework location.
After countdown and firework you have to walk back to hotel or taking taxi ( if lucky) because 95% chances will be out of taxi too.

Most of people will taking subway back. Too packed and line too long, u wont able to catch last train. 

Walk is only option.I everyear count down was park my car 20 minute walking distant away.

The next day, Jan 1 will be bored day. Everything closed

What you plan to do there so late at night? Nothing much to see as all shops will be close. Dont forget it will be freaking cold as well.
Only thing you can do is just line up to get a pass for the auction. If not mistaken you can start getting the pass at 4am (my guess).

I would not suggest to head over to the market once your flight lands, go check out the bars and have some yakitori! Warm food during winter - delicious.

Depends where do you stay for the night or you did not get any hotel booked? Shibuya and Shinjuku have lots of yakitori/izakaya that opens till quite late. Or you can think of spending a night in an onsen like Heiwajima (http://www.heiwajima-onsen.jp/en/index.html). I was there last week as I arrived at 4am in the morning. Free shuttle bus and I managed to catch some sleep as well.

There is a place called “Nonbei Yokocho” nearby Shibuya Station. Address : 1-25-10, Shibuya, Shibuya-ku Tokyo.
you can check out this website www.nonbei.tokyo

No idea about your budget, but a cab from Narita to Shibuya will cost a few hundred ringgit. And plenty! Shibuya is awesome. Think they open till 1am or 2am the last time I was there.

Not sure if it's ok to post here, but I have 3 extra data SIMs (8 days unlimited data) for Japan.

Anyone visiting Japan before the end of January and interested please PM me.