I don't think BestBuy wants to be a computer parts store. So, they make no effort to compete with Fry's, which does. They don't care about selling a lot of GPUs and would rather just sell a few (if any) to the few people that are ignorant enough to buy from them.
Fry's used to be the same. I was pleasantly surprised last November that I was able to buy am HD 6870 GPU from them for the same price as NewEgg. All of the other parts were competitively priced as well, and I bought most of my parts from them. They must have made a conscious decision to compete with the e-tailors.