Pencil Design House was a perfect place for me and my family (6 people) to stay. We were 4 adults (with my grandmother) and 2 kids (11yo, 13yo), and we had just enough space - compared to Japanese standards, the house was well structured and spacious. The photos and description give a very accurate picture of the house and the facilities. We had everything we needed in the bathroom and the kitchen as well, and it's a nice touch that we could even sit down around the kitchen table together. The location is great, a nice 10-12 minute walk from Shinjuku station, or if you don't want to walk, there's another underground line that stops only 2 minutes away. It's a great neighbourhood with many stores and restaurants nearby, and many of the sightseeign locations are easily reachable. We especially recommend Shinjuku Gyoen and Yoyogi Park which are both only a 10-15 minute walk from the flat.
The portable wifi is also a great help to get around Tokyo!