So reading Thomas's opinion he specifically says that New York's permitting scheme is essentially an unconstitutional "sensitive places" scheme because they ban the entire island of Manhattan / New York City from carry.
But expanding the category of
“sensitive places” simply to all places of public congregation
that are not isolated from law enforcement defines the cat-
egory of “sensitive places” far too broadly. Respondents’ ar-
gument would in effect exempt cities from the Second
Amendment and would eviscerate the general right to pub-
licly carry arms for self-defense that we discuss in detail
below. See Part III–B, infra. Put simply, there is no his-
torical basis for New York to effectively declare the island
of Manhattan a “sensitive place” simply because it is
crowded and protected generally by the New York City Po-
lice Department.
So I'm going with upstate permits are now valid in NYC...