Boston's advantage perhaps would be that its more similar to Seattle in terms of size and scale if Amazon is just looking for the closest East Coast version of what it has out west (and in truth DC or Atlanta would also qualify).
I must be missing something with Atlanta, Nice city but really strikes me as the epitome of a 20th century city in terms of big industry. It's very spread out and almost completely reliant on the car. It's almost like the opposite of Seattle.