As for Boston, Amazon is admittedly already adding a sizable facility in the Seaport but costs for an HQ2 and cost of living in the city would seem to disqualify.
Personally, I'd put my money on a major city that isn't a current tech hub but could become more of one.
Google is already planning it's future growth in downtown San Jose (8 million square foot "Google Village"), Adobe is expanding it's downtown SJ presence with a fourth tower, Apple and Microsoft are planning new campuses in north SJ, and Amazon is already expanding it's South Bay presence significantly. As more companies look to expand to urban, transit oriented sites, Downtown SJ will emerge as a premier location for tech company HQs.
I'm often pretty cynical (and Amazon will certainly be looking for sweetheart deals) but this seems a legitimate effort to find a location that may not be an obvious choice.
The books can be wrong, and the betting markets aren't perfect but they can be useful tool to gather what the rough consensus is at any given time.