This apartment has my full endorsement. I highly recommend it. Namio is very friendly, and always responds almost immediately to any questions you may have during your stay.
The apartment is super clean, and in a very quiet and peaceful neighbourhood of Tokyo.
As far as access goes, everything was easy to get to. At most, I spent ~30 mins on the train, with most stops I wanted to go to just 10 minutes away or less.
All in all, this is a fantastic place to stay.