I like both tbh, but I like the Ninja better, even playing on the NES version as I do. I run from a lot of the trash battles I don't care to fight in the caves/shrines, saving my spells and HP for bigger things, and the Thief/Ninja helps with that.

In a Knight/BWiz/WWiz setup, Ninja lets you get more use out of the nice weapons and armor you would probably sell otherwise, although the Master's additional inventory space for "on use" items is nice.

Black magic for a Ninja is hardly worth mentioning *except* for the fact that he can learn FAST, which can free your Black or Red Wizard up a round sooner on a few of the tougher fights (assuming you would be hasting your melee on those fights anyway).

In the NES version, Master is undoubtedly a vastly more powerful melee character turn-for-turn, but a Ninja can give you a bit more tactical diversity which can be enjoyable too.