Gooden, who missed the ticker tape parade thrown after the 1986 World Series because he was drunk and on drugs, was presented the key by Mayor Bill de Blasio during a celebration at City Hall Plaza.
"Today's a day I never thought would happen," said Gooden, "It's been a long journey, and I am grateful to be here."
Other Mets-greats also in attendance were John Franco, Barry Lyons, Bob Ojeda, Jesse Orosco, Darryl Strawberry and Mookie Wilson.
The event will be part of a documentary film about the reconciliation of Gooden and Strawberry, who recently ended a public feud.
"To have this day with my friend and the Mayor and the city we love means the world," said Strawberry.