The annual event celebrates the gay, lesbian and transgender community.
Other winners on the night included director Brett Ratner and TV shows Smash and The Amazing Race.
Madonna gave an impassioned speech to the audience about discrimination and tolerance, while dressed as a boy scout.
'When I think about young kids in America who are being bullied and tortured, who are taking their own lives because they feel alone and judged, outcast and misunderstood, I want to sit down and cry rivers of tears,' she said.
'I have teenagers of my own now, and the idea of them, or any young person experiencing that kind of pain is unfathomable to me, It's an atrocity to me. I don't accept it.'
Journalist and author Cooper was given the Vito Russo Award, named after a Glaad (Gay and Lesbian Alliance Against Defamation) founder, which is presented to an openly LGBT media professional who has made a significant difference in promoting equality.
Accepting his award, Cooper said 'being gay is certainly one of the greatest blessings' and that it had 'opened my head and heart in ways that I never could have predicted'.
Two further Glaad events will be held in Los Angeles and San Francisco to honour other media personalities.
From BBC News