This is a very nice, affordable place to stay. In terms of price, you're probably not going to find another place in Tokyo this nice AND this inexpensive. Plus, it's only a few minutes to the train station, and there's a nice little bakery on the walk over (it's called Antendo).
We were late for check-in, but luckily someone at the front was able to let us in. Be warned that after midnight, there won't be any staff at the front desk and the doors will be locked, so make sure you call in advance to make arrangements, otherwise it could get sticky if you have an evening flight in to the airport. However, check-in itself was quick, and he still took the time to thoroughly explain what we needed to know.
It is slightly chilly inside, but the beds were cozy & warm. They even had a night lamp and USB plugins. The common room is a good place to relax. They had some manga, various books, some games, a TV, and shelves of helpful travel guides (in multiple languages too). The other guests were courteous of quiet hours, and we hit it off pretty well with a couple.
There are safes available for small valuables, although the safes are in plain view of the ground floor window. Anyone peering in could easily see your combo. I had no concerns about things getting stolen, at least in this place, but make sure to be aware of your surroundings. My personal suggestion to the hotel would be to add a curtain to the window or something.
I would definitely stay here again.