I agree that in your scenario the subway (or some underground shelter) is the best place to be. One thing though in your subway example you neglect the effects of blast. Even if you are not within the fireball radius, the blast shockwave will still affect you if you are in the subway. The blast shockwave will still travel through the air and into the subway. A blast pressure greater than 5 psi can cause significant if not fatal injuries including ruptured internal organs, blood vessels, etc. and you can see that this radius will extend somewhat further out than the fireball. Also expect that a major target like NYC there will be multiple warheads detonated around the city for greater coverage.
If you manage to survive the initial blast and radiation then the great challenge becomes producing enough food through a nuclear winter, but this too is technically possible although will be difficult without a lot of cooperation globally.
And even though you have a reasonable chance of surviving the initial blast and radiation, the best most effective measure is still to prevent it from happening in the first place.