As Sun tzu already said it over 2500 years ago, Winning or Losing a fight or battle depends on the elements in the equation and how they add up.
In a clean and open fight a regular samurai would normally win. These people trained nearly every waking moment in the martial arts to be as efficient a warriors as could be in an honest and open fight.
Ninja were sneaky fighters that relied on stealth and subterfuge. The element of surprise was thier greatest weapon. As most of the ninja only did these duties as a side job they were often not as skilled as a Samurai. However one must take into account that part of the samurai took their part in the ninja's activities. SO...
Who's to say.
There's just too many blanks in the equation to solve it just in this question