Looks like there might be hope for the stained glass still:

She may not be a first lady, but Eileen Vaquilar Clifford, a soft- spoken American Airlines flight attendant, hopes to have the last word on an endangered piece of city transportation architecture, just as Jacqueline Kennedy Onassis did in the 1970s when she led a crusade to rescue Grand Central Terminal from a plan that would have obscured its facade.

Ms. Clifford’s cause is the colossal red, purple, sapphire and white stained-glass window that has greeted travelers at American Airlines Terminal 8 ever since the terminal opened in 1960 at Kennedy Airport, then known as Idlewild. The abstract modern glass facade, 23 feet high and as long as a football field, was designed by the artist Robert Sowers to create a kind of Jet Age cathedral, and when installed it was the world’s largest stained-glass structure. But for the past year it has been threatened with demolition, and its fate will be decided in the next six weeks, according to Charles Wilson, an American Airlines spokesman.
http://www.nytimes.com/2007/07/22/ny...ty/22mura.html

Looks like there's no resolution yet on the window (you'll need to read the whole article...too lengthy to post here). It might still be saved (or relocated).