Still the king.
As a reminder: tracking things like game-winning touchdowns is only interesting in a trivial sort way. I looked at all games, regular and postseason, in all leagues, from 1940 to 2012, and counted all touchdowns scored that put the player’s team ahead for good (with one exception: I did not count touchdowns scored when down by 7 and the team successfully went for two afterwards). The table below shows all players with at least 4 such game-winning touchdown passes. It won’t do much to settle the Brady/Manning debate.