What is a good idea for accomodation in Tokyo if staying there for a week?

I don't need the services of a hotel, and I want to go to the 
supermarket and self cater so hotel would be a waste of money. I also 
hate the prison-like regiment of youth hostels.

I was thinking a gaijin house or guest house? If you can pay for just 
one week they seem to be good value. What are they like? What are the 
fellow inmates like?

Also, a transport question. If you are out at night, how do you get back 
to your accomodation? Do trains run late?

thanks for any advice