HRC won "Upstate NY" only if you include Westchester. In other words, she did not.
Or if you exclude everything from Poughkeepsie (the furthest suburb of NYC south.)
Poughkeepsie may have a convenient Metro North station, but that doesn't make it a suburb of the city.
Anyway, you should check your math: Based on Leip's figures, I get a Clinton deficit of 67,000 votes for the state excluding Westchester, Long Island, and New York City, and this remains basically unchanged at 69,000 votes when Rockland, Putnam, and Dutchess counties are added.
There's plenty of room to debate "what is Upstate," but there's no way to draw the line that gives you a Clinton victory.