The ninja is a spy and assassin and works through stealth,
misdirection and blending into the surroundings. They killed with
poison and other weapons.
The samurai is a warrior who's primary weapon is the sword. They
lived by the Code of Bushido and were honorable in their means and
methods. They would kill themselves if they brought dishonor to
their master, themselves or their family.
If a ninja could overcome a samurai he would take his sword,
simply because they are better. So ninja swords are better than
samurai swords.