@Henbaka Right now I'm going to be going to school in Arakawa, which if you look at a Map of the Yamanote line, is located mainly at Nippori station, then stretches north. As for my apartment, I knew enough Japanese to google
東京 荒川区 アパート which is "Tokyo Arakawa Apartment" I tried all those gaijin sites and what not, and they just seriously overcharge. For the apartment, look at the link name under the site, as it's always in english, open a page that looks promising, and if you have firefox, add on the translation button. It'll save your skin =). I found this site, which you may be able to find your ward on. Again, translate the page if your Japanese isn't good enough. Don't try to guess the symbos too often.
http://www.atroom.jp/search_eki.php
All the way on the left hand side choice box, is single room, and then the third option down was arakwawa for me.
However, only do this if the school (which it should) is willing to talk with you and communicate with the apartment agency.
Also, please note these are mainly 2 year contracts, and for me, there is a move-in cost of around 350,000Y, which includes guarantor, key money, brokerage (at room is the agency putting you with the landlord), 2 year fire protection, insurance, deposit, and just about every other fee you can imagine.
It kills, but it's what I was saving for mainly to be greedy and live by myself.
If your cheap, like I am when I'm finished with these move-in fees, check out sakura-house.com and browse dorms, apartments, and guest rooms. I used to be in the Sendagaya dorm, located around Yoyogi station. Shared a room with four people, and payed 39,000 a month. Food was around 15,000 a month, but my mom was willing to cover that =). I would recommend finding a place eventually that isn't geared towards foreigners as you get "Japanese for foreigners" alot, and miss out on a more "real" setting I guess.
Sakura-House is easy, located right by Shinjuku station, and cheap if you are willing to share. Otherwise, look for a japanese company and try to have your school contact them for you.
Any other questions feel free to post again.