Depends what kind of accommodation and where in Tokyo.
There are basically two types: capsule hotels and hostels.
Capsules are, well, capsules. Best to google it and see what you think. Hostels are like anywhere else in the world and there are a few decent ones around Tokyo.
If you can give more of a description of what you're after I can give you a few recommendations. about 8 years ago
Capsule hotels are generally limited to men, and are the size of a generous rabbit hutch. Hostels generally tend to be grubby (at least the ones I have stayed at in Japan have been) and often have an annoying curfew. Business hotels are cheap and all over the place. Some family-run inns are cheap as well. Ther Toyoko Hotel chain is a group of cheapie business hotels. Google it and you will find one in the location you desire. If that doesn't suit your fancy, the Rakuten Travel site (google it) has a zillion reasonably-priced hotels listed. about 8 years ago
Japanese Ryokan's can be quite good. Depending on how cheap you want it, this one may be an alternative to a hotel and it's in Japanese style ie, tatami mats, Japanese screens etc http://www.tokyoryokan.com/ I haven't stayed there but have stayed in Ryokan's in Kyoto and near Mt Fuji - highly recommend the experience. about 8 years ago