I agree with guijohn. That was going to be my suggestion, if for no other reason than to rule out any medical reasons for the behavior. While you're waiting for the appointment, do some investigating.
It seems to happen only at night. Is your apartment on a busy street? Could he be seeing headlights reflected in various locations of your apartment? Are there any mirrors, prisms or other objects that tend to cause light to be refracted/reflected? Blinking electronic lights?
Ask him if he ever sees what he is afraid of in the daytime.
Maybe get a sleeping mask for him to wear at night. That would sure point you in a specific direction if he only sees the object of his fear when not wearing the sleep mask. Conversely, if he still sees and fears it while wearing the mask, that could point toward something internal rather than external. You could get some masks for yourselves too and make a game of it. Maybe give him a flashlight to use as a light saber to shine in the face of what he sees to make it go away.