First of all, it must be inside Tokyo Station. On the main street where most of JR lines leaving Tokyo Station; Yamanote Line, Chuo Line, Keihin Tohoku Line, etc, there few souvenir shops selling products from Tokyo such as Tokyo Banana, etc.
Another good place is Haneda Airport. There are two areas dedicated for souvenir shopping from Tokyo. You don't have to have an airplane ticket to purchase the souvenirs, the shops are outside of gates.
Lastly, this maybe the easiest to go, is Tokyo Sky Tree. Shopping mall called "Tokyo Solamachi" is connected to Tokyo Sky Tree and on the 2nd 4th floor are souvenir shopping area. 2nd floor is mainly snacks such as Tokyo Banana and Tokyo Sky Tree limited foods, and 4th floor is mainly crafts, cosmetics, etc.