Pope Francis kicked off his second United States stop in New York City with a Thursday evening prayer at St. Patrick's Cathedral, one of the nation's best-known churches.

Thousands of people lined up along Fifth Avenue to greet him with cheers as he made his way in his open-sided popemobile to the center of one of the nation's largest Roman Catholic archdioceses.

The cathedral's bells pealed as Francis waved to and blessed the crowd, even giving the occasional thumbs-up.

New York Gov. Andrew Cuomo , Mayor Bill de Blasio, U.S. Sen. Charles Schumer and other dignitaries greeted him on the cathedral steps.

Pope Francis landed in New York City Thursday afternoon to begin the next part of his visit to the U.S., which will take him from the United Nations to a school in East Harlem.

During the evening prayer, Francis thanked American nuns for their strength and courage in a deeply meaningful acknowledgement of their service following a years-long Vatican crackdown.

U.S. priests and sisters erupted in applause when Francis 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."

It was the strongest expression yet of his gratitude for American nuns after the Vatican under his predecessor ordered an overhaul of the largest umbrella group of U.S. sisters, accusing them of straying from church teaching. The nuns denied the charge and received an outpouring of support from American Catholics, and the crackdown ended this year, two years early, with no major changes.

Francis also expressed his solidarity with Muslims following the hajj stampede in Saudi Arabia, where more than 700 people were killed.

Francis said he wanted to offer a "sentiment of closeness in light of the tragedy" that the Muslim people had suffered on Thursday.

He also aised the clergy sex-abuse crisis, by consoling clergy for the suffering the scandal had caused them.

Francis told members of religious orders and diocesan priests that he was aware they had "suffered greatly" by having to "bear the shame" of clergy who had molested children. He thanked them for their faithful service to the church in the face of the scandal.

A group of 200 people welcomed Francis as his chartered American Airlines plane touched down at John F. Kennedy International Airport shortly after 5 p.m. Thursday.

Brooklyn Bishop Nicholas DiMarzio, five Catholic schoolchildren and other guests gathered at the airport while snipers stood atop police vehicles while a high school band played a rendition of Frank Sinatra's “New York, New York.”

Cardinal Francis Dolan of New York greeted Francis with a hug and a kiss as he arrived onto the tarmac. 

Francis then handed out mass cards and spoke with onlookers after Catholic schoolchildren presenting him with a bouquet and collection of prayers written by students in the city's 86 Catholic schools. 

After landing at the airport, Francis traveled to Manhattan by helicopter and hopped into a Fiat hatchback, traveling in the same style as he did while in Washington.

About 5 million people visit St. Patrick's each year.

Over 40 hours in New York, Francis will address world leaders at the United Nations, participate in an interfaith service at the Sept. 11 memorial and celebrate Mass at Madison Square Garden. He will visit a school in Harlem and take drive through Central Park.

It’s the first papal trip to New York since Pope Benedict XVI visited in April 2008.

The Associated Press contributed to this report.