When ordering from Amazon extra packaging is used AND fuel is used to ship it. Seems like driving and not using the extra box would have a lesser impact. Or at least in my car because the store is about 5 miles away by freeway and I drive a small, fuel-efficient vehicle.
Because Amazon don't drive the package..? Or fly it in a lot of cases? In fact Amazon has recently been moving away from USPS to "Amazon Logistics" which means even less package co-mingling/less environmental efficiency.
They send many packages on the same vehicle, and do a shortest-path route. So the marginal impact of each package is minimal compared to making a dedicated trip to Best Buy.