The result in 1940 seems to have been the result of a Willkie surge in NYC that is probably explained by regression to the mean as well as ethnic whites disgruntled by FDR's overtures against Nazi Germany.
This is correct. The isolationist vote was a factor in metropolitan NYC. There was a substantial drop in FDR's margins throughout the city between 1936 and 1940--and Willkie flipped Queens and Staten Island. Meanwhile, upstate New York simulated New England, and FDR held his vote or increased it slightly there. His statewide lead dropped from 20 points to 3.