Bond without question, he's done more missions in a staggering variety of locations and situations, is a trained marksman with nigh on every firearm and a master practitioner of Judo as well as being taught Ninjutsu in You Only Live Twice, thats the fighting style of REAL ninjas, not that clap your hands and summon a giant frog bollocks from the show that can not be named. He can pilot fighter jets and helicopters, drive tanks and other armoured vehicles as well as boats and submersibles and has regularly defeated assassins that are regarded as some of the best in the world (e.g. Scaramanga) not just the CIA. Hell in Quantum of Solace he beats a high ranking CIA agent and in the Casino/Solace storyline he's only just earned his 00 and license to kill.
Bourne, while undoubtedly skilled, is just a glorified assassin with a few flashy martial arts moves. Bond has more skill and experience. Now if it were Agent 47 gunning for Bond... THAT would be interesting.