Part of it is lots of big class 3 growers in the patient population, and a big part of it is that NY medicaid is relatively more generous when it comes to covering orthognathic surgery (and orthodontic tx in general) compared to other states, whether it's on the dental side of medical side of coverage. If a patient gets approved for the orthodontic tx, chances are they are in an income or 'need' situation where they may also have the orthognathic sx covered as well.
Though like you also said 2th MVR, there is such an abundance of surgical cases that it is definitely worth seeing if it is viable to treat some non-surgically as well for practice out in the 'real world' (especially with TADs and other treatment modalities we have now).
*And also agree.. wherever you can get in, go for it! You can get to be an excellent clinician from any program, assuming you have some self-motivation 😉.
*Edit- actually if your end goal is academia, I would try to find a program where you get a masters. I feel like that is almost a 'must have' when going into academics. (verses certificate-only programs)