Nolan > Jackson IMO.
Jackson is very competent behind the camera, but I wasn't overly enthralled by the LOTR series (except for ROTK). I think he works better as a "cult" director, because I ****ing loved Braindead, which is also one of the goriest films of all time. That said, I did enjoy the overly-verbose King Kong. Jackson knows how to work well with effects, although not always sparingly, as the awful dinosaur stampede scene in King Kong shows.
Nolan hasn't made a single film less than stellar:
Following = a fantastic debut. Not seen by many but it was ****ing brilliant for what was essentially a student film. Memento, Insomnia, Batman Begins and The Prestige all dazzled me in their owns ways. Nolan is also sparing with effects yet he has kept me enthralled and glued to the screen in every film he has made.
Jackson is more recognisably the auteur in a classical sense, although Nolan makes films that interest me more. Nolan's main problem is his editing - some of fight/chase scenes in Batman Begins were horrifically edited, made worse by the NTSC-to-PAL 4% speed conversion when released on DVD over here.