This appears to be a case of color by number, but no one appears to know what the numbers are.
One of the most commonly asked questions regarding the Empire State Building is the significance of the lighting colors and how the color schemes are decided. I wrote about the lighting schedule on March 27, 2007 in Equinox. The color schedule and meaning of the colors is easily found at the official ESB website.
In celebration of the NYU commencement, the color scheme was purple/purple/white (NYU's school colors are purple and white). The special lighting was further enhanced by the fact that the building could be seen looking up Fifth Avenue from Washington Square Park, NYU's de facto "campus."
The process as to how the decision is made, however, is shrouded in mystery. According to the New York Times, a spokesman for the Empire State Building said that the building “doesn’t discuss the intricacies of the lighting approval process.” Out of curiosity as to what is involved in having your choice of colors for lighting, I downloaded the Empire State Building Lighting Partner application. It is quite simple and straight forward. In the first paragraph you are told:
Selection as an Empire State Building Lighting Partner is at the sole discretion of the ownership and management of the Empire State Building Company L.L.C. The Empire State Building is a privately owned building—not owned by New York City or the State of New York—and, therefore, has its own policies. Selection as a Lighting Partner is a privilege, not an entitlement.
There is, however, no discussion of money, but the phrase "Lighting Partner" would lead one to believe that there is a cost. No crime there - after all, the building is a private enterprise.
There was some outrage recently when the building was lit red/yellow/red from September 30 through October 1, 2009, to commemorate the 60th anniversary of the People's Republic of China. Many speculated that it was strictly a decision based on what China was willing to pay.
NYU certainly has a lot of influence, clout and its share of controversy - see Gorillas and Cookies here. It also has a lot of money. And at least for the NYU commencement, purple is the color of money :)