While I think Bourne would win, I think Salt is being underestimated. Her H2H skills weren't too impressive relative to the generic super assassin, however her feats speak for themselves. She was able to assassinate (if she wanted to) the President of Russia, with a plan she cooked up in a very short time. Quite frankly I'm not sure Bourne could have replicated that, but of course in his world, the security would've been more realistic.
I'd say she's right up there. Then there's also the fact Salt is somewhat a female Bourne rip-off.