This is by no means any sort of "best of" list of coffee shops in Tokyo. It just happens to be the spots I visited my Tokyo trip.
Cafe Obscura Laboratory
太子堂4丁目28-9, Setagaya, Tōkyō
Just a few steps from my AirBnb, this little coffee roaster spot was the first stop for me every morning.
Mocha Coffee / モカカフェ
猿楽町 25-1 (エデイ代官山 1F), Shibuya, Tōkyō
Mocha Coffee sources their beans from Yemen, home to the owner Hussein Ahmed, who runs the cafe along with his Japanese wife.
Super quiet spot run by an old man. He'll take his time making your coffee, and you'll take your time, sit down and admire his collection of china.
Omotesando Koffee / 表参道KOFFEE
Japan, 〒150-0001 東京都渋谷区 神宮前4-15-3
Omotesando Koffee needs no introduction. Sadly, at the time of writing this, the owner has already closed up shop due to the aging of the house and the renovations required. He will be opening another coffee shop sometime this year, but in Hong Kong. Needless to say, I'm incredibly glad to have visited this beautiful space before it's gone.