Darth Vader is the father of the Star Wars characters Luke Skywalker and Princess Leia. He does not appear as a playable or a non-playable character in an Indiana Jones Lego game. He appears as a playable character in a Star Wars Lego game.
There is a reference to Darth Vader in the Indiana Jones and the Last Crusade section of the LEGO Indiana Jones: The Original Adventures video game: In the last level of the Last Crusade, the Grail Knight acts like Darth Vader at first. The Grail Knight makes the silhouette of Darth Vader and breaths like him until Indy rubs his eyes.