That will never happen. We should carefully look at where our tax dollars are going; city resident taxes should be enough to run NYCT, and the city tax paid for non-residents that work in NYC (I think this exists, paid by the employer?) should ensure that the other MTA railroads are funded.
Ultimately, the idea of democracy is to provide equal protection for all, and so NYC's relative prosperity should be funding some upstate initiatives. That said, administrative control of the subway should be entirely in NYC, and if we don't collect enough tax to run it to the standards we desire, we should be able to affect that change locally.