The "30 Rock" star wants to personally apologize to those who were in the audience that night.
During the show, Morgan said the issue of gay bullying was overblown and that if his son were gay, he would "pull out a knife and stab" his son if the boy couldn't speak to him "like a man."
He's been apologizing ever since the June 3 performance, even publicly pledging his support for gay marriage.
"I want to apologize to my fans and the gay and lesbian community for my choice of words at my recent stand-up act in Nashville," Morgan, 41, said in a statement released June 10. "I'm not a hateful person and don't condone any kind of violence against others. While I am an equal opportunity jokester, and my friends know what is in my heart, even in a comedy club this clearly went too far and was not funny in any context."
Before his trip, the Gay & Lesbian Alliance Against Defamation says Morgan will stop in New York to talk with gay, lesbian and transgender teens who have been hurt or left homeless because of parental rejection. He'll also meet with parents who have lost their children to anti-gay violence.
KABC-TV LOS ANGELES, CA contributed to this report.