Question

What is the difference between a Samurai and a ninja ?

Answer 1

Samurai or Bushi are the words reffering to warriors in feudal Japan, mostly in Edo period (1603~1807). It doesn't mean that there were no warriors before, it simply means that all of the lore and myths connected to japanese samurai warriors come mainly from that period. The same would go for their codex even though its roots date back to Muromachi period as far as I can remember. In Edo, samurai occupied one of the highest levels in national hierarchy just after the Shogun and the "puppet emperor" (emperor had no real power since the formation of shogunate (jap. bakufu). They were proud people and the only that were allowed to carry two swords with them at all times. 

Ninja on the other hand were the silent assailants in the night as some might call them. They were a part of the secret organization of master thieves and assasins working on a payroll of those who were rich enough to pay them. They were using a single straight blade (samurai were using a little bit bended swords) as well as countless types of poisons, darts, star-shaped throwables called 'shuriken' and others. 

Both of those groups are non-existent in the modern Japan, but it would be hard to imagine that there is no-one left of that abundant heritage. That is why I believe that we can safely assume that there are still ninja families present in Japan who practice their ancestors arts even if they have no use in the modern society. As for samurai, there are millions of people all over the world practicing the way of the sword, or 'kenjutsu' which is passed down from the old times. 

Answer 2

Samurai were a specific station in the caste system, they held a loyalty to a lord, but had their own lands, and were armor weilding soldiers who trained constantly. They held to specific principles and followed a Bushido code, which above all things dealt with death as an every day fact of life. , they learned archery, horsemanship, sword work, hand to hand, as well as balanced that with battlefield tactics, caligraphy, and other things that kept them focused and balanced. 
Ninja: Basically ninja were spies. That didn't hold any sort of rank in a caste system and while they may be a associated to a certain shogun, lord, or clan.you see them in TV and movies doesn't exists, there are a few books that talked  known as Ninjutsu