Historically-speaking, I prefer the ninja.
Pop-culturally-speaking, that's a difficult choice. It all comes down to who actually has it best on the Rule of Cool department? The two best choices to compare would have to be Samurai Jack and Dr. McNinja. If you can think of a better choice overall, then I welcome the discussion Otherwise, let the brain do its thing.
The thing here is that they're both scarily-good characters. Jack was trained around the world and given a sword forged by the gods in order to deal with a shapeshifting evil with a badass voice. The Doc, on the other hand, was raised by his parents...who are elite ninjas of crazy-good skill. Doc is actually so good at his ninja skills that he wants to be Batman, to the point where he ended up studying EVERYTHING at college and was into crimefighting before he became a doctor.
As per their plots, Jack's been thrust into the future and combatted an amazing amount of hordes which require either quick action, quick thinking, or both to defeat. This was all achieved despite his being an ancient samurai, which is impressive to no end. Dr. McNinja has, thus far, had to take care of...patients, pirates, raptor banditos, robots, your basic supervillains, ninjas, zombies (who might also be ninjas), time travel, dinosaurs, ghosts, giants, vampires, mafia boys, a unicorn, and King Radical.
Jack may Jump Good, but the doc's world is funnier. Still ninja.