Apparently, the music, which can be downloaded preperformance and is written by composer Mikel Rouse (no relation at all to TUAW's own Mike Rose) plays in the audience's iPods while the dancers dance (and other atmospheric sounds are added during the performance as well). Very interesting. The NYT piece seems to hint that the tracks are meant to be played in random order on each iPod, which would mean that the timing wasn't too important, but it's a cool idea (even more cool that it's done by an artist of Cunningham's age, but what else do you expect from a Mac fan?).
Definitely reminds me, too, of the MP3 Experiments done by Improv Everywhere in New York. Just goes to show you that we're still in the middle of the digital music revolution -- when we can listen to almost anything anywhere at any time, who knows what other creative folks will come up with?