I think, someday, we'll learn the truth of what happened. I just don't happen to believe that Amazon pulled the plug over some minor friction from some local protesters. That would be completely inconsistent with their operations over the last dozen years or so, and there is plenty of evidence that the move was popular(ish) in New York, generally.
OTH, I think that the protesters are basically right about what they are complaining about: pricing local residents out of the housing market, impacts on local infrastructure (e.g., crowded commute corridors), and "tax breaks" for location. I do think, however, that in the long run, it would have been a net positive for the community - but I don't live there.