My best-friend and I stayed at the Shinjuku Shared House for just over two weeks while visiting Japan for the first time and exploring Tokyo and I have to say it was one of the best experiences of our lives.
Min, the owner, is an incredibly helpful and friendly guy always a phone call, text or email away if anything goes wrong.
The immediate area has everything you need, from supermarkets and bars to local temples so no matter your reason for visiting you can find a taste of it within walking distance.
Higashi-Shinjuku Station is also less than a minute away making all of Tokyo accessible. The most time we ever spent on the subway was 35 minutes and that was getting to Odaiba. Make sure to pick up a Pasmo card for the subway system if you think you'll be using the subway to explore! We also used the "Tokyo Subway Navigation" App which is free on Android and iphone, shows you which stops to get on/off at, how much it will cost and how long each trip takes.
The apartment itself is always clean and full of interesting people. On the nights we weren't out exploring Tokyo's nightlife we'd always be able to find a handful of people in the living space ready to share a drink, food or stories.
Min does a wonderful job of making this place a relaxing and friendly environment for everyone. When I get the chance to return to Tokyo, I will also return here, brilliant fun, brilliant people, brilliant place.
If you do decide to stay here, make sure you take yourselves to the rooftop (and then up the ladder) and get a picture of the sunrise/sunset, it is absolutely stunning.