You can book a room at any Tokyo hotel through Agoda or Booking.com. I usually book my room accommodations through booking.com. Room accommodation ranges from cheap hostels to luxury hotels. Book hostels through booking.com as they have free cancellation or pay-at-the-hotel option.
If Tokyo hotel isn’t to your liking, try AirBnb. Airbnbs are immersed in neighborhoods, condos, and townhomes. There is a feeling you get when you stay in an Airbnb that makes you feel like you belong in that city or town. Since it is someone’s home, there is a certain amount of pride you feel while staying there. I have used Airbnb on some of my other trips and I loved it!
If you’re new to AirBnB, then you can get up to 42 USD free travel credit by signing up via this link.