There's a couple of very good reasons to purchase from Apple. For one thing, if you want to return or exchange the product, Best Buy will charge you a restocking fee, and Apple will not. Apple is also a lot more flexible when it comes to returns or exchanges. There's a 14 day return policy, but usually they will be ok with 30 days as well.
Secondly, if you want to purchase Apple's One to One plan (please look it up on apple.com to see what that entails) you can not do so if you've purchased your Mac at Best Buy.
Otherwise, you've got a year of Apple Care either way, and can extend the Apple care for an additional two years anytime between the date of purchase or a year from that time. Honestly, if you don't care about One to One service, and want the insurance plan from Best Buy, then there's nothing wrong with that.
However, I would not trust Geek Squad techs with my Mac vs an Apple Genius. They simply don't have the same training and that counts for a lot to me.
Doug