[Japoncito]

Best way I've found to get an apartment in Tokyo is to go through agencies that specialise in short term stays for foreigners. I would recommend Sakura House. They mostly provide Guest Houses, which are a type of shared housing, but they also have a lot of apartments on offer as well, in all parts of Tokyo.

If you try to obtain an apartment through a strictly Japanese real estate it can be really expensive. The local etiquette here is to give the agent a few months rent up front as a gift!

Definitely check out Sakura House, and i'm sure there are other similar websites but I just can't think of them.