At the top would be the emperor, but he is usually no more than a figurehead with true power residing in the shogun who is warlord for all Japan.
The shogun really came to in his own during the warring-states period. Daimyo fought wars with each other for whatever reason. This era ended when the shogun would visit each daimyo and come away with a hostage who stayed in his court.
Next in terms of power would be the daimyo or the local feudal lords. They owned the land and reaped the profits from them.
The samurai served the daimyo, fought in wars and died on command if necessary. Only the samurai were allowed weapons, all others were subject to on the spot executions.
Farmers, merchants and peasants all defered to the samurai.
For more info:
http://en.wikipedia.org/wiki/Samurai
http://en.wikipedia.org/wiki/Daimyo
http://en.wikipedia.org/wiki/Shogun
http://en.wikipedia.org/wiki/History_of_Japan