Well, if this is an overall question...I'd say that both of them are probably incomparable to each other. Think about it this way: Bond is a British CIA agent who performs missions around the world and sleeps with ladies often. Indiana Jones is an archaeologist who finds himself in dangerous situations underground or deep in unexplored territory of mankind. It's not exactly easy to compare these two objectively. <_<
Also, I haven't watched much of either completely, so I'm probably not the person to ask if you want anything other than my personal opinion.
But, if you're asking me personally...Indiana Jones.
1) He's a Ph.D. That means that he's spent years studying in college and universities and learning things, which makes him super awesome. I respect guys who have a sharp, sharp brain.
2) He uses ONLY a whip and a pistol to get out of the situations he runs into. Compared to Bond, that really means he's using his head and relies less on devices and so forth to get out. So, MAJOR MAJOR kudos to Indiana Jones.
3) He's morally stronger. He's not a womanizer of any sort, and he actually makes himself a man of decent character even as a superhero. Awesome, because there aren't a lot of humble guys out there.
4) He is actually more human. He has flaws that make him more realistic as a person, even if his stunts are a bit gravity-defying, and that makes him a strong character and leaves awesome memories of his coolness.
Indiana Jones, DEFINITELY.
