In Spielberg's classic Jaws there is a scene when Hooper and Brody find Ben (they'll wish their fathers had never met their mothers), Garndner's boat floating apparently abandoned. When Hooper goes to look at the hull and finds the shark tooth, Ben's head floats down scaring Hooper into dropping the tooth, however Ben is missing an eye. I don't know how Ben dies, be it drowning or whatever, but how does he manage to lose and eye?
When the boat crashed outside of Amity, the impact of the shark hitting the boat may have caused Ben Gardner to fall over, and he could have simply had bad luck and knocked his eye out on a sharp edge or a fishhook. Or, there is always the thought of underwater creatures picking parts off of his body. Hope this helps.