Depends on the Ninja clan. The Iga clan is different and has a big mark in history, check it out. Samurais are hired guns on salary, their code is very selective, not all samurais are created equal.
So with that said and the myths out of the way...between the 2 the ninja is just the better.
How much weed were they smoking when they believed they had magic ninpou and shit. Samurais were gangster af, basically one of the ruling clase of Feudal Japan or something since the Emperor/Ruler was merely in name while the military mostly controlled everything else.
Samurai movies tend to be better than Ninja movies, I mean, ninja movies can be fun in a campy grind house sort of way, but Samurai films were like high art in comparison, I also love Yakuza movies