My favorite coffee in Tokyo is Turret Coffee near Tsukiji Market. The seasonal latte at the moment is a Christmas inspired Buche de Noel with berries and a hint of rum.
If you go be sure to check out the turret parked inside. It’s the vehicle used at the market for deliveries.
Turret Coffee
Chūō-ku, Tsukiji 2-12-6
Food Sake Tokyo 
That was our favorite coffee on our visit to Tokyo as well. Looking forward to visiting Turret again when we return in the fall.
PS: love receiving your blog. So much wonderful information!
Lisa
Arigato! Happy holidays. Stay warm. Turret is my favorite coffee in Tokyo!
Happy holidays to you too!