Trip.com M.
Google
Really loved this hostel. The people at the front desk are wonderful, and it looks like it is out of the way, but the closest metro station is actually a loop line (non JR) through Tokyo, which has most of the stops directly accessible, and the walk is quite pleasant. You can even see Skytree from the terrace in the evenings.The rooms aren't too crowded and has bathrooms and showers just for your room, which made it very easy and you didn't have to keep searching for a free bathroom. The dorm room also came with a little kitchen too, and quite a few amenities (hair dryer etc).