Mr. Pipes is perhaps best known for Campus Watch, a national initiative he created to scrutinize Middle Eastern programs at colleges and universities. The drive has accused professors of, among other things, being soft on militant Islam and sympathetic to the Palestinian cause. It has stirred widespread controversy and, in some cases, may have undermined professors’ bids for tenure.

Mr. Pipes was joined in the monitoring effort by other self-declared watchdogs of militant Islam. Their Web sites are often linked to one another and their messages interwoven. One critic, David Horowitz, founded Islamo-Fascism Awareness Week, a campaign aimed at college campuses. He noted in an interview that monitors of radical Islam have increasingly trained their sights on nonviolent Muslim-Americans.

“They don’t throw bombs, but they create political cover for ideological support of this jihadi movement,” he said.

Mr. Pipes places Muslims in three categories, he said: those who are violent, those who are moderate and those in the middle. It is this middle group, he argued, that now poses the greatest threat to American values.

“Are these people who are not using violence but who are not fully enthusiastic about this country and its mores, its culture — are they on our side or are they on the other side?” he asked.

Ms. Almontaser never considered herself unenthusiastic about America, she said. But as the conflict over the Khalil Gibran school intensified, she came to be seen by many through Mr. Pipes’s lens. In his article in The Sun, he referred to Ms. Almontaser by her birth name, Dhabah, and called her views “extremist.” He cited an article in which she was quoted as saying about 9/11, “I don’t recognize the people who committed the attacks as either Arabs or Muslims.” (As The Jewish Week later reported, Mr. Pipes left out the second half of the quote: “Those people who did it have stolen my identity as an Arab and have stolen my religion.”)

The Stop the Madrassa Coalition focused primarily on Ms. Almontaser as a strategy, said Mr. Pipes, because the group could get little information about the school itself. The coalition quickly publicized several discoveries. Ms. Almontaser had accepted an award from the Council on American-Islamic Relations, a national Muslim organization that critics claim has ties to terrorist groups (an assertion the group adamantly denies). In news articles, Ms. Almontaser had been critical of American foreign policy and police tactics in fighting terrorism. She also gave $2,000 to Representative Cynthia A. McKinney of Georgia, whom Mr. Pipes and others have characterized as an Islamist sympathizer. (Ms. McKinney, who is no longer in office and did not respond to requests for an interview, has had a strong following among Arab-Americans in part because of her criticism of the Patriot Act.)