This... I'm originally from New York, and I know lots of good engineers who grew up there, but quickly realized that you don't make anything more for working in New York versus San Francisco, Austin, or Denver.
Yes, you can afford a place in Manhattan on an engineer's salary. But it's going to be too small for a family, and if you want a bigger place you're going to need to do a long commute. Compare that with other cities where a well-paid software engineer is at the top end of the income ladder and can rent out a full house for what they'd pay for a 2-bedroom in NY.
(And yes, it's even a lot more expensive than SF. I've looked at apartments in both cities - while rents in SF are comparable to New York, you're still generally getting a much larger place for the same price. That matters if you have kids.)
Brooklyn and Queens are nice (if not that much cheaper for the areas near Manhattan.) But if working in New York means you have to live 40 mins outside of Manhattan, or in Hoboken / NJ, what's the point of being in NY? Might as well be in Denver with a 4000 sq ft house.
It's unlikely that NY rents are going to drop a lot. If startups in NY want to attract more top talent, they're going to have to pay significantly more than startups in cheaper locales.