I’d definitely recommend staying at Masami’s place, Calm House. It’s great value, and an awesome little spot.
It’s located in Hatagaya, an easygoing and very charming neighborhood, but it’s only two stops (10 min) to Shinjuku Station. From there, you can get anywhere in Tokyo, and Shinjuku itself (the area around the station) is fantastic for food, drink, or whatever else you could want.
The room itself is lovely. It has everything you need and the bed & linens are nice! Most importantly, as hosts Masami & Masahito were easy to communicate with and very helpful.