I thought you were poking fun at Saitama but these look really good.

Tokyo has good third wave coffee shops if you're not looking for a meal set but the coffee itself
https://tokyocoffee.org/category/area-guides/
https://en.goodcoffee.me/area/tokyo/
I usually stop by Glitch to buy some beans for friends who love third wave coffee (I don't drink coffee myself, so secondhand recommendation).

+ksandness rec. Look for a kissaten. I believe smoking is technically allowed if that's an issue.
https://en.wikipedia.org/wiki/Kissaten
https://www.youtube.com/watch?v=g6K_C122zpQ

There's also NaNa's Green Tea which is a Japanese chain oriented towards matcha & hojicha if you're looking for tea.
nana's green tea