We used https://www.tokyofreeguide.org/ many years ago. Our guide was a retired postal employee who guided to improve his english, which was already excellent. All we had to do was cover his expenses and ours. We used the subway for transport. We asked where he would like to go for lunch, and he took us to a fabulous eel restaurant, which seemed to be very popular due to its long line. We were the only non-japanese guests.