People work really hard in Tokyo. Many times I saw passengers on the metro falling asleep, some even while standing. I prefer to take it easy, have a good nights sleep and then pick a beautiful work spot to get some things done. My favorite work spots in Tokyo have huge windows with amazing views; an experience in itself and a privilege to work from there for a (half) day.
The Academy Hills Library Cafe on the 49th floor of the famous Roppongi Hills building offers a breathtaking 180 degree view over the city. A day membership is 2000 yen (€16). You’ll feel a part of the privileged Tokyo working/studying crowd who work here in serious silence. There is a cafe, but you can also bring your own food and drinks. The Library Cafe is often rented out for private meetings, so check if it’s open the day you want to go.