Jackie Chan is the better athlete; he trained as a boy at the Peking Opera school to be a stage performer, to include martial arts, acrobatics, stunts, etc. When you see him doing a backflip or falling thirty feet and landing on his head, that's Jackie Chan doing that.
Jet Li was trained strictly in the martial arts -- specifically Wushu. He's a natural, and rather phenomenal, pure martial artist. BUT, he's not a stuntman; when you see Jet Li fall thirty feet, that's his stuntman, not him. He has said many times in interviews, "I'm an actor, not a stunt man."
So the two are very different in terms of abilities. But the question is who is the better fighter, and the answer is Jet Li. In terms of pure martial arts ability he's a 10 on a scale of 10; the guy was just born to be a martial artist. Chan, on the other hand, is more like a 7. His training wasn't primarily martial arts; his training was to perform on a stage.
I'm reminded of the movie Drunken Master 2. The original director was legendary Hong Kong martial arts filmmaker Lau Kar Leung, a gifted and highly respected martial artist himself whose training lineage can be traced all the way back to real life Chinese folk hero Wong Fei Hung, considered one of the few legitimate kung fu masters. On the set, Lau was constantly having to correct Chan on proper style and form. So often in fact that Chan got frustrated and fired Lau, then took over the directing himself.
At any rate, while Chan may be a better athlete and stuntman, in terms of straight up martial arts skill and fighting ability, Jet Li's got it all over him. He's better trained in pure fighting and is a great deal faster; some directors have commented about having to ask Li to slow down his movements when filming because he's so fast, the camera doesn't always catch his movements. Add that speed to his pure martial arts ability and you've got a guy born to kick ***.