Graybeard, I had posted more of the rough transcript of FDNY communications earlier in this thread, but these two entries suggest that they knew it was a commercial airliner.
1529hrs- Bronx receiving numerous calls for an explosion from a commercial aircraft over the borough.
1530hrs- Bronx transmitted (2) boxes for an explosion from an aircraft. Bronx CO advising B/C's that Queens CO is in constant contact with Airport Tower and are monitoring the aircraft which is attempting to conduct an emergency landing.
Posting on the Web of the FDNY communications radio traffic began at 1537 hours, so it was quite contemporaneous.
Manhattan- Aircraft Down In River 01-15-09 - EMTBravo.net