Both games are very difficult, but for different reasons. Ninja gaiden requires you to be extremely quick and you will die many times despite not knowing where or who hit you. Dark souls, in that manner, is more fair. You understand who hits you, and how they did it. Don't confuse that with it being simple though, Dark Souls will have many enemies that can do half of your health in a single hit, and some (mostly bosses) can wipe out your health in a single hit. In Dark souls, it is possible to simply die from not knowing what to do.
Ultimately, I believe that Ninja Gaiden would be more difficult on the master ninja level, but Dark Souls doesn't use the leveled difficulty (everyone has the same difficulty to start with), so I would say that if you were playing ninja gaiden on a lower level then Dark Souls might be more difficult for you. Not to mention that it can take up to around 50-70 hours to complete. I suggest trying it though, it is alot of fun and there is no harm in trying.