We stayed at DoMo J and it was a great launching point for seeing the rest of Tokyo. Head to Higashi-Shinjuku station and you have quick access to anywhere else you want to visit.
The apartment was clean and surprisingly quiet, I thought it might be kind of loud based on the location. It's definitely an upgrade from staying at a hotel with the extra living space but is still very small. Your knees will touch the wall when you sit in the bathroom. The beds are very hard as well. Those are small complaints for such a nice room and location.