I think you are double counting Queens and Brooklyn in that estimate of Long Island because between the Metro areas of just Buffalo and Rochester is over 2 million people not counting places like Syracuse and Albany.

Yes, New York like most States is full of dozens and dozens of counties with less than 10,000 people but they add up and while the city proper of Buffalo is like 1/10th a single Borough in population, it too has suburbs and exurbs. Even the area around Fort Drum is just over 100k people.