The offer of accommodation in Tokyo is quite varied. You will find many international hotel chains, where prices are also upscale. If you are looking for something cheaper, look for a local hotel. They offer simple, but clean rooms, to local businessmen. They welcome foreigner travelers as well.
In Tokyo you will also find the traditional Japanese hotels, or Ryokans, most of them offer Western and/or Japanese rooms. In these small hotels you will have the oportunity to relax in a Japanese sauna.
Tokyo has some Youth hostels, for backpackers.