So, you're postulating that there is something of a Simpson's paradox going on in NYC between two largely separate cultures -- that of people with college degrees, and that without? This is theoretically possible, but conveniently not directly testable due to secret ballots. It is however indirectly testable in two different ways -- and the numbers still don't back you up.

1) Exit polling (https://www.timesunion.com/capitol/article/voted-trump-new-y...) does not back you up. More college educated New Yorkers reported voting for Trump than total fraction of San Franciscans that voted for Trump.

2) Middlesex County, Massachusetts (roughly, the north half of greater Boston) is an alternative example to NYC that has a very similar proportion of college degrees compared to SFO (about 1% less). Middlesex County is in the northeast. About 42% of those voters voted for Trump, which is more than New York and more than double SFO. Suffolk County (with Boston proper) has very similar numbers to NYC for both college education and voting for Trump. This can't be explained as a cultural difference between NYC and Boston because the Suffolk ratios are so similar. It can't be explained as an educational difference between SFO and Boston because the Middlesex educational numbers are so similar but there are proportionally more Trump voters than NYC. It can't be explained as a cultural difference between Suffolk and Middlesex because first, they are direct neighbors sharing a public transit system, and second, Middlesex is considerably more traditionally leftist than Suffolk (leaning on that cultural difference would undermine your original argument).