At one of the city's biggest and oldest mosques, Imam Shamsi Ali called for forgiveness in a time of "hatred and animosity between people."
And he urged his congregation to remember the nearly 3,000 people killed on 9/11, whose anniversary just happens to coincide with the movable feast of Eid al-Fitr this year.
"Today is supposedly a day of celebration for Muslims, a day of happiness", the imam said in his sermon at the Harlem mosque.
"But we are all reminded of an event that took place nine years ago", he said. "This is more than just a celebration -- this is a day of reflection."
About 2,000 men and women crammed into two separate rooms prostrated themselves in their prayers on the carpeted floor of the mosque. Sunlight poured in through high windows under the central dome onto pale green walls.
The mosque was filled to overflowing with more than a hundred people praying on the grass outside while non-Muslim New Yorkers streamed past in noisy rush-hour traffic.
Worshippers said they felt under siege after months of controversy over plans to build an Islamic cultural center and mosque two blocks from Ground Zero and now the ugly row over Pastor Terry Jones' Koran-burning threat.
According to Amnesty International, the human rights watchdog, US Muslims face growing "fear" and "persecution."
"I've been here four years and this year we feel a bit excluded. There are challenges", said Fairuz Saadun, 32, a banker.
Saadun, like other worshippers, said he was frustrated at the message promoted by opponents of the Ground Zero mosque that the 9/11 attack was representative of all Muslims.
"We know it's not rational. It's only a small group of people who don't understand Islam, that we don't promote violence, that we're like Jews or Christians and want peace", Saadun said.
"You have to have the right perspective: 9/11 and Islam are two different things."
The Ground Zero Islamic center is the brainchild of Feisal Abdul Rauf, a New York imam known for years of attempts at building bridges between the Western and Islamic worlds.
He says the center would show Islam's positive face in the same neighborhood where Islamist hijackers slammed two airliners into the Twin Towers.
The project won the support of New York Mayor Michael Bloomberg and President Barack Obama. But opposition is snowballing, fueled by right-wing radio hosts and politicians looking to deal Obama's Democrats a heavy defeat in the November 2 middterm congressional elections.
Some opponents say a mosque would be insensitive to the memory of those killed in the World Trade Center, while the most outspoken activists describe the proposed mosque as a monument to terrorism.
Jones' now suspended threat to burn the Koran could trigger global protests by Muslims and so alarmed the Obama administration that Defense Secretary Robert Gates made a personal appeal to the pastor on Thursday.
Now Jones is attempting to use his notoriety to force a meeting in New York with Rauf, saying the imam should agree to move his planned Islamic center further from Ground Zero in exchange for cancellation of the planned Koran burning.
Mohamed Zohny, who sells Islamic clothing, said after prayers in Harlem that demands to move the Islamic center from the Ground Zero area attacked a key constitutional right.
"Everyone is free to have a religion," he said. "In there we're going to be praying for people who were in the World Trade Center."
Rehan Khan, a 36-year-old health executive attending prayers with his two boys of six, said Muslims were seen as barely human.
"A lot of people tend to think we're cold and heartless", he said. "Are people forgetting that Muslims died on 9/11. Do their souls not count?"
Amnesty urged the US authorities to stamp out what it said was growing Islamophobia.
"In a climate of fear and perceived external threat, it is essential that the authorities step up measures to ensure that people from all communities, whether citizens or not, are equally protected", the organization said in a statement.
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