We stayed at Mokoto's place twice because we loved it so much the first time.
This is by fat the biggest place we have stayed in Tokyo.
Mokoto is very generous in supplying good quality essentials, like towels, sheets, cleaning supplies and hygiene items, in abundance. We hardly needed to buy anything during our 1-month-plus stay.
The place is super-clean, with each room having its own stick-type vacuum cleaner ready to be used.
There are two train stations within easy walking distance, and you can walk to Tokyo Skytree if you don't mind enjoying a 30-minue casual walk.
I highly recommend Makoto's place.