The articles you mention all refer to recreational "model aircraft". Do you have the actual statutes?
Here's an article that suggests that commercial flights are allowed, which makes sense.
The 5 Best Parks To Fly Your Drone In NYC – In The Field
Here's something I found which exempts commercial aircraft with regards to flying near correctional facilities and delegates it to the FAA:
New York State Senate S2125
BILL NUMBER: S2125
TITLE OF BILL : An act to amend the correction law, in relation to
civilian drone use near a correctional facility
PURPOSE :
To prohibit civilian drone use within one thousand feet of a
correctional facility.
SUMMARY OF PROVISIONS :
Section 1 amends the correction law by adding a new section 625
prohibiting drone use within 1000 feet of a correctional facility or a
local correctional facility in this state. This section also defines
the term drone pursuant to this provision and provides penalties for
violating this law.
This prohibition shall not apply to the operation of a drone by any
person or entity that the federal aviation administration has
authorized to operate a drone from commercial purpose, where the drone
is operated in a manner that complies with that authorization.