There's alot of difference between the various knights of Feudal Europe, take a Polish knight with their lighter armor than a regular knight and a Pike, or a German Knight fully clad with plate mail and a zweihander!
The Samurai themselves preferred the use of a Yari, rather than katana. This means that however agile they may be, they still can only hit the delicate areas of the armor.
Theres too much to think about when you're thinking of such a thing to even begin to predict who would win. You've got to think about field conditions. You also have to think about whether either side has any information on the other regarding field tactics, weaponary, armor etc. If that's not the case then either side is going to be very weary of the others capabilities.
Even after all that you have to think about that both these two legendary warriors built, their armor, weapons devised their tactics becuase they were under different conditions. They're very different and so built their startegy to best defeat their opponent, not each other.
(But If I had to go with one i'd go with the samurai :P)