What does it mean for a ATC to say a flight's callsign followed by "in disguise"?
The controller was probably referring to an airplane in a different livery but operating under the American call sign.

A likely example is US Airways. After the two companies merged, from October 2015 all flights were operated under the American call sign, but re-painting the US Airways planes took at least a couple years.

This is not standard phraseology but "Kennedy Steve" is known for trying to inject some humor into his work. See also: What does Top 1% mentioned by ATC refer to?