I travel through Tokyo Station almost five times a week. Until recently getting a really good cup of coffee in the morning has been a challenge. Finally there is a great little shop serving coffee by Sarutahiko Coffee in Ebisu (Ebisu 1-6-6). Standby opens at 7 a.m. which is often the time I am getting to the station as I make my way to Tsukiji Market. The shop is hard to find, but persevere for it is worth it. The shop is near the South Entrance to the Shinkansen inside of Tokyo Station. If you have an early morning train out of Tokyo, be sure to allow yourself some time to pick up a cup of coffee at Standby. There is a narrow seating area in the back of the shop if you want to rest your feet.
Chiyoda-ku, Marunouchi 1-9-1, 1st Floor inside of Tokyo Station (near South Entrance to the Shinkansen)