Daley--and here's why:
Rescuing Chicago was much more of an uphill battle than rescuing New York. Chicago is in the less-reknowned midwest, it has been much more dependent on manufacturing than New York has, and it probably lost a bigger chunk of its population than New York had by the time Daley took over.
New York had natural advantages for Guiliani to work with--a much bigger media center, more large companies, and its preeminence as the financial powerhouse that it is. This is not to mention its location on the job-rich east coast with all of its universities and corporations. Oh, and the nation's capital is only a few hours away by train.
With Chicago, a city that looked like it was about to collapse, Daley excecuted a turnaround that I think will go down in the history of cities. He turned a crumbling midwestern industrial center into a world-class city ripe with new businesses, great global corporations, a financial hub (the booming options/futures exchanges), and a corporate services sector that continues to slowly replace Chicago's manufacturing base. He also created a huge nidus for arts and theater that attracted major dance troups, artists, and is slowly turning Chicago into a theater center on par with the best in the world.
Obviously, New York takes these things for granted. But Chicago had to work its ass off to be what it currently is, and I give Daley a lot of credit for turning a rusty old city into the great metropolis that it has become