To those interested,
I couldn't find green tea kitkat in Ameyoko st in Ueno or the shop in Tokyo 1st Avenue Ramen st.
If you dont mind travelling a bit, we did find some green tea and sakura green tea kitkats in Aqua City mall in Odaiba.
4th floor..look for a shop called Gift Trip i think.
They even have Tokyo bananas.
Hope this helps! :-)