Bloomberg said on his weekly radio show on WOR that it is inappropriate for a government entity "to look at somebody's political views and decide whether or not they can live in the city, or operate a business in the city, or work for somebody in the city."
The billionaire businessman-turned-politician was asked about comments from Boston Mayor Thomas Menino, Chicago Mayor Rahm Emanuel and San Francisco Mayor Edwin Lee criticizing Chick-fil-A.
Chick-fil-A president Dan Cathy angered gay-rights advocates, including the mayors, when he said the company was "guilty as charged" for backing "the biblical definition of a family." He later added, "I think we are inviting God's judgment on our nation when we shake our fist at him and say, `We know better than you as to what constitutes a marriage."'
Emanuel said "Chick-fil-A values are not Chicago values," and Menino wrote in a letter to Cathy: "There is no place for discrimination on Boston's Freedom Trail and no place for your company alongside it."
Lee tweeted Thursday: "Closest (hash)ChickFilA to San Francisco is 40 miles away & I strongly recommend that they not try to come any closer."
Bloomberg said Menino, Emanuel and Lee are "really are good mayors" but "trampling on the freedom to marry whoever you want is exactly the same as trampling on your freedom to open a store."
Richard Socarides, a New York lawyer and former Clinton White House adviser on gay rights who is urging a boycott of Chick-fil-A, said Bloomberg is right.
"Consumers can disagree with a company's corporate political position and decide not to spend money there," Socarides said. "But the city cannot regulate speech by denying someone a permit to operate their business just because you disagree with their political beliefs."
Menino has more recently said he was expressing his own opinion and acknowledged there is little he can do to prevent the chain from coming to Boston.
A spokeswoman for Emanuel said that while the Chicago mayor believes that Cathy does not share his city's values, he would not block Chick-fil-A from opening a new restaurant.
Most of the Atlanta-based Chick-fil-A's restaurants are in the Bible Belt. There are none in San Francisco or Boston, and there is one in Chicago and one in New York City.
Bloomberg said that if the chain wanted to open a second New York City eatery, it would have to apply for the necessary permits.
He added that he has never eaten at Chick-fil-A himself.
All four of the mayors are strong supporters of gay marriage. Bloomberg officiated at the wedding of two male aides when New York legalized same-sex marriage last year.