Technically, they're rooting for the same team, if by "team" you mean "a group of players forming one side in a competitive game or sport." But that's not what we mean! Governor Cuomo is rooting for the New York Giants, while Chris Christie, apparently, is rooting for the New Jersey Giants, which is a team that does not exist. If the fictitious New Jersey Giants win the Super Bowl, Christie wants the victory parade to take place in New Jersey, instead of Manhattan.
Christie is trying to make a point, and to be fair, it's a legitimate one: The New York Giants, despite the name, have played their home games in East Rutherford, New Jersey, since 1976. Common sense dictates that perhaps they should be known as the New Jersey Giants. And yet, they don't seem to want to be. Take the hint, Christie.