One of those tales that is more fun because it doesn't really give an accurate comparison of the two aircraft's capabilities! The PR9, great aeroplane though it was, topped out at around 60,000'. The U2 - as Mike Hale recalls - operated routinely considerably higher than that.
Well, according to Wikipedia, the Canberra held the world altitude record of 70310 feet in 1957. Now, I doubt that was a typical Canberra, it was probably tweaked (if not heavily modified!) to achieve that, but it demonstrates that it was capable of going higher quite a few years ago.
According to some of the RAF bods I talked to (and I can't remember the exact details, but it wasn't down the pub!) the PR9 had been modified substantially from the older variants to increase its capabilities, including it's ceiling.
Of course, the exact performance characteristics of both aircraft were classified, and so no one knows (or is at liberty to discuss, yet) the exact ceilings, and I suspect even then it would be heavily caveated in terms of of payload and how willing you were to take the aircraft into a dodgy flight regime eg the oft discussed Coffin Corner of the U2. I doubt the PR9 was capable of exceeding the limits of the U2, given that the aerodynamic construction of the U2 is more suggestive of high altitude operations than the relatively short wings of the Canberra, but it may have been capable of approaching it under some circumstances.