Having done both, I'm a firm believer in Horses for Courses.
If you have the opportunity you should definitely try both, to find out which type of flying your body is best suited to - then listen to what it's telling you.
The good news is, despite all the scare stories, no-one has ever proved one type of flying does more permanent harm to health than the other. This assumes you take the precautions indicated by the life-style e.g. drink plenty of water and use sun screen for long-haul, take meal and other breaks whenever possible and live within reasonable distance of base for short-haul.