This weekend marks the 50th anniversary of the Stonewall uprising on June 28, 1969.
Gaga, wearing thigh-high rainbow boots and a Versace jacket, talked to the large crowd for about 15 minutes and thanked them for their support, but she did not perform.
"This is a historic day. You should be so, so proud of yourselves," she said, choking back tears. "Look around you. Look what you have done.... it makes me cry. I am so emotional today. This community has fought and continues to fight a war of acceptance, a war of tolerance, and the most relentless bravery - you are the definition of courage."
Whoopi Goldberg and Chelsea Clinton also addressed the crowd, while Alicia Keys and others performed.
iHeartMedia New York partnered with LGBTQ social advocacy and community engagement organization Pride Live for the second annual Stonewall Day Concert.
Stonewall Day is global campaign to elevate awareness and support for the Stonewall legacy and the continuing fight for full equality for the community.