Let me elaborate on Charles' statement. The "ninja" as known in popular culture didn't exist, so your question is mood at the get-go. However, your question has some other problems.
With both ninja and samurai, you had those who were blademasters, as well as many who never entered combat. This question is so general that it is impossible to answer conclusively, like those endless rapier-vs-katana arguments.
If you meant on a whole, here's how you find out: hire fifty kenjitsu swordsmen, and pit them one on one against real ninjitsu students (good luck finding real ones; many don't even call their art ninjistu anymore due to the Mcdojos). Then, come back and tell us how the tournament went.
[This message has been edited by Benjamin1986 (edited 02-14-2005).]