Nop. You only can entering to Japan from tour Group which depart from Malaysia. Your Visa for entering Japan only can be done by HIS / JTB group tour package.
If you transit at Tokyo, you only can stay inside transit hall which is currently 90% of shop are closing. I suggest you tapao more food from Malaysia.
If your transit to US flight was 2 days later, i suggest you change the date ASAP. If not you will stay overnight inside Transit hall for 2 - 3 days like Tom Hans Terminal Movie.

You can do stop-over in Japan enroute to US but your flight to US must depart on the same day too because NRT will close at midnight while HND is 24hrs Airport.

In other words, you short layover on Airside would be your only chance of set foot into Japan without getting into trouble (unless the govt decide to open everything)

Center / Downtown will be very expensive.  What is your Budget?
Want cheap hotel can stay at Ikebukuro.  You want even cheaper can stay at Kitasenju.

i prefer Hotels.com and i always use this platform because of the free one night after collecting ten nights of booking and the price guarantee (if you found a cheaper price elsewhere, they will refund the price difference to you).

You can use the platform to list the hotels based on nearest to farthest location, lowest to highest price, etc.

I have used it countless times in various countries (including Japan and China) and never experienced them saying they don't recognise the booking. I even received several free nights stay and price difference reductions.

I always used those third party platforms to talk to the hotel receptionist because most of the time they don't speak English and they dont reply my emails. So i relied on the help centre agents of the platform to get the answers i want. They will call the hotel and speak in their language and then they will get back to me.

Since you just travelling alone, i suggest to just stay in business hotel like toyoko / sotetsu inn to save some money. The extra money can spend on food