I had the absolute best time at Satoshi and Hitomi's apartment. They are both incredibly kind and nice, always willing to take the time to make sure you have the best possible time on your trip and help with any questions you may have.
Right from the start they were great, picking me up from the bus station and treating me to a delicious home cooked dinner. They are very friendly and respectful of the guest's space and privacy.
You cannot find better hosts than Satoshi and Hitomi, I definitely recommend their listing if you are considering travelling to Tokyo.