You can get the green tea flavor at Uwajimaya, but I think they aren't the same as the ones you can get in Japan. I had some a co-worker brought back from a trip and they were mild and nice, and the kind I bought at the store were a little too grassy tasting.
A co worker brought in Japanese fruit flavored Kit Kats in one day. I think she found them at World Market. The strawberry one was pretty good but the others were odd.
Whenever my parents have a layover in Japan they stock up on kit kats. I'll have to tell them to look for some of the weirder favors next time! They usually just get strawberry and green tea.