In Japan, you can find so many individual cafes on the back street, far away from tourist area. If you want a quiet place to relax around Skytree area, I recommended this small cafe.
The main theme of this cafe is wood mix nature. They also sell organic vegetables and handmade displays. The only thing I don't like Japanese cafe and restaurant is that you still can smoke indoor. I hope the government will make a new law about indoor smoking soon. Otherwise, even a good environment will be ruined by the smelling.
This cafe is called - Cafe Kohana, it is near B3 exit if you take a tube (underground). The outlook of the shop is not that eye-catching, so you might easily miss it when you walking pass. There are about 6 seats in the cafe. If you want free WIFI, then this will not be your spot. In Japan, I feel it is not as easy as in London to find a free Wifi coffee shop. In London, you can go into almost every single Pret or Costa to get free Wifi, but here the only safe choice in Japan is to go to Starbucks. (Personally, I don't like their coffee, expensive and weak). But they do have some sesaonal limited flavour that tastes interesting.
It is not difficult to find a special coffee shop in Japan, each of them has their own personality. I really enjoy a afternoon with a cup of coffee, reading some blogs, and watching outside.