The Ninja House is certainly unique and a great pick for those looking for an interesting peek into Japanese living.
It is about a 6 minute walk from Hatagaya station, which is about 2 stops from the major Shinjuku station (trains from here can take you almost anywhere in Tokyo.) The area itself is quiet and with some exploring, you won't be disappointed by the shops and eateries you'll find.
You will have a fantastic time climbing up and down the Ninja House and discovering the areas and little touches that make this place special.
Shin is a thoughtful host & neighbor. Easy to communicate with and is more than willing to help and give recommendations to make your stay in Tokyo enjoyable.
Tip: carefully make it out into the roof to see a great view of Tokyo skyscrapers and the area. The many konbini nearby will also help provide you with the snacks you need for a memorable rooftop picnic!