tokyo is huge and with that description you basically included Chiba as well, you're talking about an area that would take an hour or more to cross by train.There are love hotels absolutely everywhere which will run you about 10,000yen per night, or there are business hotels which are around 5,000 to 7,000yen a night but are frequently booked in advance. There are also capsule hotels but I have not actually ever come across one while just walking around so I can't advise you about that.
There are dozens and dozens of cheap backpacker hotels and youth hostels but they are generally not very clean. They are however 2,000 to 3,000yen a night so if you just need a place to crash for the night they might be a good choice. New Koyo located in Minami Senju is one example. There are dozens of hotels like it in the same area if you walk around and look for them.
