Well, I think everyone knows where I stand on this issue.
Of course, I go with Magnum. The stories and the characters really stand the test of time for me. Plus, it's important to remember that Magnum was the first time a major character---the hero, in fact--was a Vietnam vet. Up the that point, Vietnam vets had been victims or monsters, to be feared or pitied. I also am very fond Quantum Leap, but after awhile, the stories became too repetitive and nothing ever really changed much; I always knew Sam would succeed and leap to the next character.
On Magnum, major characters died. Relationships changed. Magnum was a good, heroic character, but he killed an unarmed man. He mooched off his friends and was something of a deadbeat. He was loyal and kind, but could sometimes be childish.
Sam wasn't given much chance to be anything but unerringly good. I actually thought Al was much more interesting of a character--he was flawed but still a good guy. Sam wasn't allowed to have many flaws because he had to always save the day. I think that's why I liked the QL finale when so many others didn't. Sam didn't win in the end, but sacrificed everything to help Al.
I like both shows, but Magnum was a huge influence on me as a kid. Quantum Leap was just a really fun show I watched for awhile.