I just did a quick google search, so I'm not sure how official this is, but according to [url=http://dolyen.ldblog.jp/archives/32081808.html]this site[/url], the popularity ranking is as follows:
1. Yubari Melon
2. Strawberry Cheesecake
3. Blueberry Cheesecake
4. Tochiotome (Strawberry)
5. Kobe Pudding
6. Uji Green Tea
7. Shinshu Apple
8. Purple Sweet Potato
9. Yamagata Cherry
10. Sweet Potato
It may be worth noting that most of these are seasonal or regional specialties, so personally, I've only seen the Uji matcha, Kobe pudding, and sweet potato flavors. And if you take "most widely available" as a measure of popularity, the ones I see most are green tea, white chocolate, and dark chocolate. These are also the only varieties commonly available in my local supermarket - conbini and touristy places tend to have a bit more variety.
Price is going to depend on where you get them (I think I've seen them in 100yen shops?), what size package you get, and how limited edition they are. Within Japan, I think Amazon is probably your best bet, as with most online shopping... outside of Japan, I'm not sure, but I'd probably start at your local Amazon or eBay. If you'd like to try a bunch of flavors at once, you can also find variety packs on Japanese import sites like this one: http://whiterabbitexpress.com/ultimate-japanese-kit-kat-variety-pack-15-x-2-flavors/
