From the article:
Eric Phillips, a spokesman for Mayor Bill de Blasio, tweeted that the flight stopped in Mecca, which is experiencing a flu outbreak, and "early indications point to that as a possibility."
Bollocks to that. Mecca doesn't even have an airport, flights to Mecca use Jeddah airport.
The aircraft in question (A380, A6-EUF) has last been in Jeddah on 25 August, but this flight definitely did not "stop" in Mecca, or anywhere else enroute.
Also, the common incubation period for influenza is 2 days. So even if some virus survived on board and infected the passengers, they would probably not have shown symptoms upon arrival already.
At best, I would imagine there were a few passengers on board, who have been in Mecca 2-3 days before flying to NYC, and may have caught the flu there.
None are more hopelessly enslaved than those who falsely believe they are free.
(Johann Wolfgang von Goethe)