I do not see how there is even a debate here.
1. James Bond is hired muscle, a government stooge. No matter how awesome he is, he's only badass because the Queen owns his ass. Indiana Jones is a self-made man, a teacher who conducts his badassery on his own terms, because he believes that precious artifacts should be in a museum instead of in the hands of Nazis.
2. Indiana Jones fights Nazis, the evillest people on Earth (and yeah, I know he fights Commies in the new movie but I haven't seen it yet, and let's just forget "Temple of Doom" exists). James Bond fights against whomever his government is against, again because he is the Queen's little bitch. Many Communists (and now, I guess, unspecified Middle Eastern "terrorists") were good people. Ergo, Indiana is more moral than Bond.
3. Indiana ain't afraid to get his hands dirty. Aside from snakes, there's nothing Indiana fears. James Bond's machismo hides a deep seated neuroticism that manifests itself in foppish habits, an uptight manner, and incredibly unstable relationships with women. Indiana is also friends with Jonathan Rhys-Davies, who was excellent in Sliders.
4. The proper way to serve a martini is stirred not shaken.
5. Dude, Last Crusade. Come on, dude.