well, hm...
ninjas can hold weapons in both hands, and throw things... plus their speedy...and in ffIII, theyre the ultimate "fighter" class, can equip any weapon/armor.
samurai have cointoss, useful if you have money to spare. they also can equip katanas (masamune anyone?) and have power lowering techniques (like auron's for example.)
or are we talking about real life? i wouldnt want either. ninjas in real life were little more than gardeners, and being a samurai would be too much work. (not to mention that theyre all gone anyway...)
now, on the other hand, if i could have my own masamune...