I had a great stay at Sakura Hotel Hatagaya.
Pros: literally a two-minute walk to the Hatagaya train station and then two stops to Shinjuku station (not covered by JR pass, but very cheap), attentive and friendly staff, very cheap for a hotel this close to Shinjuku, on-site washers and dryers, lots of small shops, restaurants, and convenience stores nearby
Cons: super small rooms even for Tokyo, almost nowhere to put clothes, hard to get the water adjusted to the right temp for a shower, food in the hotel restaurant was so-so
Overall, I enjoyed my stay here and would stay again. If you need a short stay in a convenient location and are on a tight budget, this place is perfect. I had a couple of issues with the fridge in the room and with the heat, but both issues were taken care of quickly. There are only two washers and dryers for the whole hotel, so there were a couple of times I wanted to do laundry but couldn’t because the washers and dryers were in use. But, still, way more convenient than having to do laundry off-site. My return flight got unexpectedly cancelled in the middle of the night and the staff worked with me until 3AM to make alternate arrangements during that time. They were also willing to work with me if I had to stay an extra day-which fortunately I didn’t. I was allowed a late check out because of the circumstances. I speak Japanese, but mostly communicated in English because the staff all speak excellent English.