Governor Andrew Cuomo's long-time partner announced back in May that she had been diagnosed with breast cancer in March.
She underwent a double mastectomy, but had a set back with an infection.
"He pulled me out of the audience at the end of the mass and gave me a special blessing," Lee said. She added that it was a "huge surprise".
Just days ago, the Food Network star announced that she is "cancer free".
She told "Good Morning America's" Robin Roberts, "My doctors have said that I am cancer free and that I am ready to go."
Lee shared her excitement about Pope Francis' visit and her choice in outfit for the occasion on her Facebook page.
They will be joining the pope when he visits with the families of victims at the 9/11 Memorial and Museum on Friday.