I'm surprised that no one has mentioned Pittsburgh yet. uber did some early self driving pilots there. CMU is there. Google has a large office there. Amazon has also started hiring software engineers for an office in Pittsburgh too. Cost of living is very cheap. Many upsides to Pittsburgh. I don't know what the city could afford in terms of subsidies though.
There's also available suburban sites in Southern NJ and Malvern, PA that are accessible via mass transit, the Navy Yard (which desperately needs a subway spur) and tons of developable/reclaimable industrial space in North Philly.
Given how accommodating PHL has been with Comcast, I'm sure Amazon could get what they need.