"We had a great stay at APA Shinjuku Gyoemmae. It is in a truly unbeatable location and the staff at the front desk are wonderful. The hotel even has umbrellas to borrow. It's very convenient to get around the city using the metro from here, and there are also great spots to shop and eat close by.
For travelers used to western hotels, the room is extremely small. Typical for Tokyo but definitely a shock as a first-time visitor. Both the bedroom and bathroom are quite tight, and I hit my head on the sink during a shower one night. That said, the staff kept the room clean and well-maintained so we were as comfortable as we could be.
If you want to use the hotel onsen (public bath/spa), note that tattoos are not permitted. This is unusual for the area as several other Shinjuku onsens/sentos do permit tattooed guests. This was disappointing but I respected the rules."