Great small place in an excellent location with everything you need.
Yes, the room is directly next to the train line, and your body will adjust to the noise - But that's part of what makes it convenient. Takahafudo is located just 30 mins outside of Shinjuku, 15 from Hachioji/Tachikawa/Tama Centre.
You can save money and cook for yourself using the induction heater (The large black pan is the one that works with it properly). The town is very relaxed and there's also a great running path just infront of the property which you could run up to a marathon on if you're really keen.