That kind of behavior is referred to and might be permitted by the SCOTUS decision 'tptacek cied above. Relevant paragraph:

Whatever the permissible scope of intrusiveness of a routine border search might be, searches of this kind may in certain circumstances take place not only at the border itself, but at its functional equivalents as well. For 273273 example, searches at an established station near the border, at a point marking the confluence of two or more roads that extend from the border, might be functional equivalents of border searches. For another example, a search of the passengers and cargo of an airplane arriving at a St. Louis airport after a nonstop flight from Mexico City would clearly be the functional equivalent of a border search.[4]*

There are certainly important differences: the court gives the example of a search of passengers that definitively crossed a border and who are searched where they disembark.

That being said, since NY is a major international travel hub, the searches described in that article might qualify as "functionally equivalent" to border searches. In any case, I think it's a stretch to say that DHS treats everything 100 miles from the border as a "Constitution-free zone". Have we seen equivalent searches being performed in Georgia or Virginia?

The reason I singled out the train as a particular case is that it's clearly domestic travel, not international. If there are foreigners on board, they'd have to come through some other border crossing before getting on the train. You can't get to Penn Station from outside the country without going through customs somewhere else, most likely an airport. Which means that this is not equivalent to a border crossing, unless you adopt a meaning of those terms so vague that anything within 100 miles of the border is the functional equivalent of a border crossing, which seems to be what the border patrol is doing.

And yes, it is possible to find places in the country, even in the 100-mile zone, where DHS is not engaged in abusive activity. That's cold comfort to folks who have to deal with them when they are.

ETA: if you're wondering about international train travel, like from Canada, I've taken one of those trains, from Montreal to New York. (Very scenic route, right down the shore of Lake Champlain.) The border-crossing inspection happened in Vermont, outside St. Albans, within minutes of where the train crossed the border. That's what "functionally equivalent to a border crossing" means, if it means anything at all.

I cited the examples of Georgia and Virginia to emphasize that known cases of these Border Patrol operations seem to cluster in areas that are frequently points of disembarkation for international travel.

I don't disagree with you that DHS operations are often abusive, and I have even suggested that the examples cited by that article might not be justified as "functionally equivalent". I do think, however, that the idea of a "Constitution-free zone" isn't a useful concept for describing DHS practices.

Well NYC is an embarkation point for international travelers to the USA, is it not? I'm not sure that searching a passenger on a train from NYC is inherently more infringing on liberties than searching a passenger on a van from the Mexican border, as both "start points" for travel are very much borders of the U.S.