I believe the only direct flights from NY to Morocco are on Royal Air Maroc, to Casablanca. But it sometimes is less expensive if you go through London on another carrier. The desert MAY be cooler in early October, but I about croaked from the heat in Merzouga while camping near there on one trip at that time of year.

We took Royal Air Maroc from NY if I remember correctly we landed in Marrakesh 3 years ago, then left from Casa to go home. We really liked Royal Air Maroc. We're from Baltimore, MD. My husband did a lot of research and found that the best flights from our area (NY/DC/Balt) land in Casa or Marrakesh (we take a similar route and tried really hard to land at one end or the other but we were either ending up too far away, paying too much or had extra lay-overs). You can also get good flights out of Washington, DC or BWI (in Baltimore) but beware - connector flights in New York can be a bit of a hassle (got stuck there trying to get to DC for 4 hours last year).