[1][3] The location of the accident, and the fact that it took place only two months after the September 11 attacks on the World Trade Center in nearby Manhattan, initially spawned fears of another terrorist attack, but the National Transportation Safety Board (NTSB) attributed the disaster to the first officer's overuse of rudder controls in response to wake turbulence from a preceding Japan Airlines Boeing 747-400 that took off minutes before it.

[4]: xi, 135  The stabilizer separated from the aircraft and fell into Jamaica Bay, about 1 mi (1.6 km) north of the main wreckage site.

The loss of engines cut power to the FDR at 9:16:01, while the cockpit voice recorder (CVR), using an emergency bus, stopped at 9:16:14.8 upon impact with the ground.

Among the details that Jabarah offered to authorities was a claim that Khalid Sheikh Mohammed's lieutenant had told him that Richard Reid and Abderraouf Jdey had been enlisted by al Qaeda to execute identical shoe-bombing plots as part of a second wave of attacks against the United States.

[18][17] According to NTSB spokesman Ted Lopatkiewicz, the weight of the memo's veracity was questioned, as no evidence of a terrorist traveling on board was found.

The evidence suggested that the aircraft was destroyed after a piece of the tail assembly, "the vertical fin, came off," while it did not indicate "any kind of event in the cabin.

The NTSB concluded that the enormous stress on the vertical stabilizer was due to the first officer's "unnecessary and excessive" rudder inputs, and not the wake turbulence caused by the 747.

[21] Contributing factors were characteristics of the Airbus A300-600's sensitive rudder system design and elements of the American Airlines Advanced Aircraft Maneuvering Training Program.

This, coupled with two events earlier in the life of the aircraft, namely delamination in part of the vertical stabilizer prior to its delivery from Airbus's Toulouse factory, and an encounter with heavy turbulence in 1994, caused investigators to examine the use of composites.

[23] The possibility that the composite materials might not be as strong as previously supposed was a cause of concern, as they are used in other areas of the plane, including the engine mounting and the wings.

The resulting hazardous sideslip angle led to extremely high aerodynamic loads that separated the vertical stabilizer.

If the first officer had stopped moving the rudder at any time before the vertical stabilizer failed, the aircraft would have leveled out on its own, and the accident would have been avoided.

[27] The aircraft performance study indicated that when the vertical stabilizer finally detached, the aerodynamic loads caused by the first officer's actions produced 203,000 pounds-force (900 kilonewtons) of force on the rudder, meaning that the vertical stabilizer did not fail until far in excess of the 100,000 lbf (440 kN) of force defined by the design envelope.

[21] The Allied Pilots Association, in its submission to the NTSB, argued that the unusual sensitivity of the rudder mechanism amounted to a design flaw that Airbus should have communicated to the airline.

The NTSB indicated that American Airlines' Advanced Aircraft Maneuvering Program (AAMP) tended to exaggerate the effects of wake turbulence on large aircraft, creating a simulation scenario whereby turbulence from a 747 creates a 90° roll (rather than the likely 5 to 10° roll, though not explaining this to the pilots) to maximize the training challenge.

[21] According to author Amy Fraher, this led to concerns of whether it was appropriate for the AAMP to be placing such importance on "the role of flight simulators in teaching airplane upset recovery at all.

[7] One of the victims, Hilda Yolanda Mayol, had previously survived the September 11 attacks, having escaped from the North Tower of the World Trade Center.

[38] The authorities at John F. Kennedy International Airport used the JFK Ramada Plaza to house relatives and friends of the victims of the crash.

"[41]: 2  David Rivas, a New York City travel agency owner, said, "For the Dominican to go to Santo Domingo during Christmas and summer is like the Muslims going to Mecca.

Dominicans continued to book travel on the flights[41]: 4  until American Airlines ended services between JFK and Santo Domingo on April 1, 2013.

A ceremony commemorating the disaster is held annually at the memorial every November 12, featuring a reading of the names of those killed aboard the aircraft and on the ground, with a formal moment of silence observed at 9:16 am, the estimated time of the crash.

[47] Atop the memorial is a quotation, in both Spanish and English, from Dominican poet Pedro Mir: "Después no quiero más que paz" (which translates to "Afterwards I want nothing more than peace").

[48] In a ceremony held on May 6, 2007, at Woodlawn Cemetery in the Bronx, 889 unidentified fragments of human remains of the victims of the crash were entombed in a group of four mausoleum crypts.