Assuming decent airflow in your rig, then pound-for-pound (money) a top-end air cooler will perform better in terms of cooling, and similarly in terms of noise.
With a cramped case, the extra airflow from the all-in-one water system might mean lower temps for other components, but it's not certain and you can get around with extra fans/better cable routing etc. with an air system.
The big, heavy air solutions cause some people concern about stresses on the motherboard (never been that bothered myself, but don't move my PC much).
For my money, the best thing about the all-in-ones (and the reason I've just side-graded to one) is that they take up so much less space, look nicer (IMO) and contribute to whole-case cooling if set up correctly.
I'm extremely happy with mine (Antec 620) - I just wish I could find a similarly-priced and easy-to-use set for a HIS HD 5850

Love that card but it's the loudest, hottest thing in my case by a country mile. If I could get a cheap loop on there I think I'd be all but silent except under extreme load.