Best Buy usually has slightly (slightly) lower prices than the Apple Store, but you have to be careful. You will find the BB salespeople rather less informed than you might like, and they will try to upsell you hard on accessories and BB's own service agreements. I don't know about the open box issue, but it wouldn't surprise me from BB. It's buyer beware for sure.
For me, buying from the Apple Store provides extra peace of mind. BTW, I can highly recommend B&H PhotoVideo in New York as a very reputable dealer. They are an authorized Apple reseller and their prices as are as good as you will find anywhere. In all my years of dealing with them, and the thousands of $$ of equipment I have purchased from them, including Mac and pc purchases, I have never had a problem even once! B&H is one of my very favorite vendors.
NOTE: I do not receive any compensation for recommending B&H, Apple or any other vendor. I'm just a very satisfied customer.