It genuinely doesn't matter, but in the case of Black Friday deals, you're better off picking up all of your gadgetry from Best Buy at a severely discounted price. There is no real advantage of buying from either Apple or Best Buy, other than smaller price tags at the latter, given that Apple rarely ever lowers its prices unless there is a newer design on the market.
Best Buy is an official Apple retailer, so you can rest assured you will be getting the same product from either store. Best Buy is also now an official repair center for Apple products, so you can even go there for repairs if your iPhone or Apple Watch is defective.