Crystal City and Newark are next door to massive tech areas. In VA there are tons of DoD/Military tech organizations and NYC is right next door to Newark. It's probably cheaper to plant themselves next to those hubs than inside of them.

* Added: Especially if you factor in all the people that would normally commute into NYC or DC/Arlington from the surrounding areas now commuting to a potentially closer office location. Could be really big for lots of people (and of course Amazon).