I usually go to the ones south of MINAMI-SENJU station which is a little bit east of Ueno in a rather down-market area. On the way to Narita Airport. I’m sure many of you know the area.
A room can be had for around 3,200 yen or less per night. Shared bathroom and shower and sink. If you are lucky you’ll get a fridge and a TV. Some of the cheaper hotels have no air-conditioners. The least I ever paid was 1,800 yen in a type of day-laborer hostel filled with, well, day laborers, mostly older alcoholics. I liked it. It was clean and neat, near a park. I liked being able to drink at 7:00 am outdoors, sitting on a bench with such companionable fellows.
The hotels in this area cater to backpackers from Western countries, Japanese students, cheapskate Chinese and poor people. Why do I say the Chinese are such misers? The rooms are THREE TATAMI MATS in size and I have seen 3 Chinese in one room. Friendly, nice people. I befriended them on one occasion and gave them beer.
https://en.wikipedia.org/wiki/San%27ya