I've not read it to completion, but the YoRHa: Pearl Harbour Descent (depicting events leading up to NieR: Automata) is certainly very good. As an aside, the NieR: Automata light novels are excellent.

If you're in to your Yoko Taro there's also several manga entries in the Drakenguard universe, but I don't know these so well.

There's also a bunch of good adaptations of visual novels, like Danganropa and Steins;Gate, but I feel like I'm cheating a little by suggesting those!