I stayed at Kura hostel for 9 nights as a young solo female traveler. I felt really safe, the accommodations are really fine and tidy. The main corridor may be a little bit narrow but it will get you closer to your neighbors ;) !
The situation is really good, quiet and close to everything at the same time. The neighbourhood is the-true-Tokyo-like, and it feels good to come back here in the evening after a long day in some touristy parts of the city !
Every member of the staff is great, discreet and helpful. I felt really comfortable in this hostel and I recommend it if you are travelling in Japan on a budget.