The Shizuoka Prefecture "antenna shop" located in the Tokyo Koutsu Kaikan building (Yurakucho) started selling them in December of last year. Here is their announcement, in Japanese:
Look for the interestingly named "Shizuoka Mt.Fuji Green-tea Plaza" in the basement.
google map: http://goo.gl/maps/XswKF
Pretty sure you can't find them in Tokyo. Pretty sure you can only get those in Shizuoka. But sometimes certain department stores or train stations have food fairs where they sell gift food items from different parts of Japan... I think you'd only be able to buy unagi pie in Tokyo through special sale events like that.
Can't you settle for Home Pie or Genji Pie? I know they're not the same, but close enough. You can find them in just about any supermarket.