The Ninja House was definitely an unique stay. It can be challenging for you to get used to it at first but afterwards, only amusement and fun. The rooftop is the best feature and you will be able to enjoy the view of a Japanese local neighborhood. The space was enough for our group of 3 girls but can be a bit cramped if you are of bigger builds. There are many shops and small restaurants/eateries around so it will be very easy for you to find a late night snacks or a nice place for meals.
Shin-san was extremely friendly and helpful. He went out of his way to assist us with many things and to that we thank him alot :) I will definitely recommend you to stay at his place for your trip in Tokyo!