Well the ninja has stealth but almost no armor, The Samurai has heavy armor which none of the ninjas tool can penetrate.
The only way the ninja could win would to get the Samurai's armor off, that would be impossible because anything thats near that Samurai will be hit buy its super fast sword. The Samurai would win.
Yea but thats not a fight, thats a assassination, and Ninjas cant run up 10 ft wall and bounce off doing a backflip and kick him in the head, thats all Hollywood.