There are many coffee shops that are delicious but I thought OBSCURA coffee is delicious.
The shop is in Akihabara, Setagaya, Sangenjaya, and Hiroshima.
Another recommendation is Cafe Kitsune in Omotesando.
Their theme of decor is "Japanese style". I am sure you can relax at this cafe! They also have various Hoji-cha, and Matcha drinks :)
Do you mean cafe or coffee bean shop?
There are many cafes in Tokyo. I like old style cafe called “Jun Kissa (純喫茶)” by Japanese.
Almost every area in Tokyo has some Jun Kissa, but my favorite area to go for Jun Kissa is “Jinbocho”.
Jimbocho is called as “City of Book”. There are many Jun Kissa, because I think books cannot be without coffee.
For example, Kura has a good atmosphere in Jinbocho.
Other famous cafes including Jun Kissa are listed here: