According to Computer & Videogames reading of EDGE magazine (go internet!) the LEGO Indiana Jones games with be sans swastika, just like the LEGO sets. Developer Traveller's Tales says that LEGO has replaced the Nazis with "an anonymous genocidal, occultist, trenchcoat-wearing master-race."
On the one hand I get it: LEGO is a Danish company and Europeans are understandably more touchy about representing the Reich in pop culture (and it's a safe business decision, besides). On the other hand, if they were fine in the movie and the movie is fine for kids, what's the big deal?
Lego Indy: First concrete details [ComputerAndVideogames.com]