Three generations of our family (5 adults, 2 kids under 6) stayed at Keiko's apartment. The apartment was larger than I expected and certainly big enough for our group. The apartment is a few stops from Shinjuku and is a short walk to the metro, on a line that also includes the Tokyo station. This made getting to and from the apartment very easy.
Our children enjoyed the local playgrounds; one directly opposite and another a block away. The local fire museum is a good family option on a wet day.
Keiko was friendly and helpful, and ensured that we enjoyed our time in Tokyo.