Tokyo Station

You can find a wide variety of souvenirs, mostly foods and lifestyle goods, at shops and department stores inside or near Tokyo Station.

If you don't have time to go outside of the station, try "e-cute". They have nicely designed boxes of snacks and foods. http://www.ecute.jp/tokyo/

For something new and cool, I recommend checking shops at KITTE, a new shopping facility at Japan Post building outside the station.
http://jptower-kitte.jp/ My favourite is a lifestyle store CLASKA.

There are also Daimaru department store (for foods) directly connected to the station, and Marunouchi Buildings (for fashion) a minute walk from the station.