Who would win in a fight between a knight and a ninja?

A ninja would win because they are mostly light and agile, while a knight wearing over 50lbs of armor would be slow and open for quick attacks. Knights were very good fighters but became obsolete after quicker and more skilled fighting styles were introduced to mid-evil warfare.

I disagree.
A fully equip knight in late period plate (ie about the same time period as the early Samurai and Ninjas) is pretty fast moving as well as armoured - shape of plate rather than weight being the key - and he has a shield, a longsword (which is a good weapon, designed for fighting on foot or horse and in a long melee), and probably a mace of some sort for close in work.

What removed knights from the top of the food chain wasn't lighter, better troops it was decent projectile weaponry which didn't require long training from childhood to use, ie Guns and Crossbows, and the training and drilling of cheaper more numerous troops, Pikemen especially. This leads to mass armies rather than household troops and the end of the single combat that knights were best at.

They become Heavy Cavalry, drilled soldiers rather than individual heroes, that still have a place in warfare for another 700-800 years. (The last charge of lance armed cavalry in the British army being successfully delivered during the opening stages of the First World War!).