First, be sure you know which Kona you are getting when you compare prices. There is Kaufman Kona (which is the preferred one, I think) and Kona Bay Kona. Kaufman is more expensive. Also be sure you are comparing the same widths.
I usually buy from
http://www.fabric.com but the very best time to buy is when Hancock's of Paducah has their annual sale (which I think is sometime in December or January). At last year's sale they put Kaufman Kona on sale, plus I got something like a 30% discount off the sale price and free shipping. If I remember correctly, it ended up being something like $2/yard. That website is
http://www.hancocks-paducah.com/ . Just be sure to realize, when you are shopping this Hancocks, that their prices are all in *half* yards.
Edit: Also be aware that there is always at least one coupon for fabric.com that you can add for additional savings. Google "fabric.com coupon code" before placing your order, and also check their website's coupon page (usually listed at the bottom of a page) to get a code.