Can't picture Boston not being in the final 3 for this, assuming several things beyond what the company has already stated.
1) Amazon won't want another HQ on the west coast (so no SF or LA).
2) Bezos is too liberal to give HQ to Trump loons (so no Austin, Charlotte, or Atl)
3) Amazon needs an already thriving metropolis, and not a dump (so no Philly, Baltimore, Detroit, etc)
By that measure you're looking at places like Denver, Minny, Toronto, Chicago, Boston, NY and DC which isn't getting enough mention.
I find it hard to picture for political reasons locating in Canada. The negative press would be brutal despite our friendship with our northern neighbors. Chicago is a shooting gallery in a state in about the worst fiscal condition of any other. There's also brutal political infighting going on that will probably prevent a decent bid from being put forward. I've read that Denver doesn't have a strong tech base but I don't know that first hand.
That would leave me with front runner DC, which has better airports, a transit system that works, a similar cost of living, a bunch of tech talent with all the government employees there, and the fact that he owns the Post. The only drawbacks would be space (have no idea but know you can't build skyscrapers in DC due to height restrictions) and I'm uncertain how the tax incentives would work there.
NY vs Boston is a jump ball. Seems like they've been competing a lot lately (GE, Aetna) and it would depend on what size city and cost of living Amazon would like to locate in. Boston is a lot more similar to Seattle than NYC is in terms of size but that could cut both ways. I would put Minny as the dark horse in all of this. They might just sneak in.