D.T.
I would instantly suspect he has some sort of skin irritation there. Like he hasn't gotten the soap off of his face or somehow he's developed a yeast infection there or it spread from somewhere else. My middle boy has one spot on the back of his head that is just susceptible to yeast.
If you truly believe it's a habit then I would swab his eyes with a cold wet cotton ball everytime you see him rubbing them. Be as unemotional as possible when you do so he doesn't use it as an attention getter.