When I first arrived in Tokyo I needed temporary accommodation for the first month. I called a foreign support service called ESLC and they arranged everything for me. They collect a percentage from the appartment owner so I didn't need to pay an introduction fee or anything. They also gave me a lot of free advice on visas etc. Everyone there speaks English so if you don't speak Japanese that's no problem. Even if you don't take their accommodation they will still give you advice so it's worth giving them a call.
Their office is in Ikebukuro. The number I have for them is +81-3-6909-4120.
I cant remember the company email address but you can contact Mimura san at
[email protected] (that's the mail address on the business card she gave me).
Anyway, have a great time in Tokyo!