JR,
You didn't include your departure point and NY is a big area. I normally would have said that Skyline and Blue Ridge are kind of a diversion. While not a bad diversion and if your starting point is well west of the Hudson, it might not be much of a diversion at all.
Do be aware that some of the tunnels of the Blue Ridge are kind of low clearance. If you are leaving soon, be aware that the southern leaf peepers will be out in force.
We did that run from Cherokee to Front Royal and didn't pay to camp anywhere.
That was 10 years ago and we need to do it again.
Matt