Oh boy, been there. Luckily you have someone between you and him, so I would work closely with your department head and make sure you are protected from the worst of the narcissistic behavior. I'll take your word for it that it's more than always talking about himself.
I had a boss who was not only narcissistic, but also had paranoid personality disorder ("I am awesome, and everyone is out to get me!"). I was one of her direct reports. There is no way to win, you only become more and more miserable, the speed being determined by the amount of direct power they have over you. As much as you say you want to stay, I can say from experience that it is not worth it, no matter how much you value the mission, the work you do, etc. The worst things about Ns is that they steadily erode one's own self-confidence and feelings of worth. I should have quit the minute the depths of her toxic behavior became clear.
Confronting the N is NOT a good idea- they will see it as a threat and go after you. I was sure that the CEO and board at this NGO would realize the negative impact of this one person after 10 (10!) people quit, one after another, over the course of 3 years, but no, they only saw the cachet that her research brought them (even though she was full of shit about that too).
Sorry and best of luck. Don't sacrifice your own mental health because of someone else's mental illness.