Perhaps most galling to the Bill Donohue and the Catholic League was last year, when the tower was lit in red to recognize the 60th anniversary of the People's Republic of China, "Even though 77 million innocent men, women and children were murdered under Mao Zedong,'' said Donohue.
While the selection process seems cloaked in secrecy, one example of an application denied became public last year, when an Iranian activist group applied to have the top of the building bathed in green light to protest Iranian President Mahmoud Ahmadinejad, who was visiting the United Nations at the time.
That group was given no explanation for the denial, according to a Wall Street Journal article, which also said that Malkin tries to stay out of political disputes.
The Iranian activists got their green lights anyway, thanks to some fortuitous timing: the Iranian president's visit coincided with the "Emerald Gala," in honor of the 70th anniversary of the release of The Wizard of Oz.
The controversy over commemorating Mother Teresa has many scratching their heads.
"This is not a religious request,'' said City Councilman Peter Vallone Jr., one of the authors of today's resolution. "Mother Teresa is possibly the greatest humanitarian the world has ever seen."
Privately, some close to the controversy are saying that Anthony Malkin has a personal beef with Donohue. But Donohue says he had never heard of Malkin prior to the rejection and he surmises that it may have more to do with anti-Catholic sentiment.
"It smacks of bigotry,'' he said.
"Given the fact that Mr. Malkin is identified with the pro-choice community, it's not a great leap of faith to conclude that it's his pro-abortion passion that has something to with his decision to stiff Mother Teresa. We've seen this before. It doesn't take a rocket science to connect the dots"
The Malkin Fund gave more than $4 million to nearly 400 charitable organizations in 2008, the latest year for which tax filings are publically available. The donations included small sums to reproductive rights groups.
Mother Teresa, a Catholic nun of Albanian origin, has been recognized worldwide for her humanitarian work on behalf of the poor, the homeless, people with HIV and AIDS, leprosy, orphans and others in need. But she was also controversial for her work opposing abortion and contraception.