On Friday he will address world leaders at the United Nations, participate in an inter-faith service at the September 11 memorial and celebrate Mass at Madison Square Garden.
Francis will also visit a school in Harlem and drive through the famous Central Park.
Thousands of well-wishers lined the streets leading to St Patrick's to greet him before the service.
The pontiff told American nuns that he wanted to thank them for their strength, spirit and courage and to "tell you that I love you very much".
This is a siginificant expession of thanks for US nuns after the Vatican under his predecessor ordered an overhaul of the largest umbrella group of US sisters, and accused them of straying from church teaching.
Many nuns denied this and were supported by other American Catholics, as a result the crackdown ended this year, two years early, without any major changes.
Speaking to Congress in Washington D.C. the Pope urged people to share America's wealth with the less fortunate.
He will finish his visit this weekend in Philadelphia, when he speaks in front of Independence Hall and celebrates Mass on the Benjamin Franklin Parkway to close out a big Catholic family rally.
He has already spoken out about a number of issues including climate change and immigration.
Francis condemned arms sales too.
Speaking in English he emphasised that the US needs to embrace immigration: saying the US was founded by foreigners "who came to this land to pursue their dream of building a future in freedom.
"Let us treat others with the same passion and compassion with which we want to be treated," he said. "Let us seek for others the same possibilities which we seek for ourselves."
