When I moved from Fukuoka to Tokyo I used Sakura house to have a starting point rather then rent a hotel while I searched for an apartment. I stayed in a private apartment not a dorm. I must admit the one I received had a filthy kitchen, apart from that I can't really complain. There's no smoking in the rooms and your not allowed to let anyone stay the night so it didn't really feel like my own space but I was able to organize everything without being in Tokyo and move in straightaway so I cant really complain. It good to get started but like Kaeru said expensive.

I can tell you a company NOT to use:
http://www.tokyocityapartments.com/
http://www.fontana-apt.co.jp/

They are the same company (using the same office) running under 2 different names.(Suspicious from the start if you ask me)

These guys are crooks, I left my apartment cleaner then when I got it, it was also pretty filthy when i received it but they still charged a 25000 yen cleaning fee (I bleached the whole place, it was gorgeous).

Their office is filthy and unprofessional. If your talking to them in person and the phone rings they put YOU, the person in the office in front of them, on hold for 10 to 15 minutes.

They blamed some damage on me that was already there when I moved in and charged me

They left me waiting for 5 hours on the moving out date, i set a time and date a month in advance, confirmed it day before and they still forget, i had to ring them after they were 4 hours late and it turns out they had forgotten and made me wait another hour.

They charged me the incorrect amount for rent and then came to my apartment demanding more money

I was supposed to have a TV, they promised to bring me one the next day but never did.

They make you turn on your gas water and electricity and make you turn it off before moving out. This wasn't really a problem for me but although the gas, water and electricity departs claim to speak English I had to do it all in Japanese.

There's more but you get the point. Don't every use TokyoCityApartments/Fontana