Much like Cthulhu.
The Likely Solution:
The very first investigation of the incident Occam's razored the shit out of the "mystery": There was a storm, the trio was out securing their lighthouse-keeping gear, and a large wave or a freak gust of wind swept them out into the raging sea.
"In a nice, sheltered place like this? Impossible! Now, about those aliens ..."
-a conspiracy theorist somewhere
"But what about the uneaten meal and all the signs that clearly point in the direction of [insert crazy theory here]?" you ask. And it would be a good question, if it wasn't for the fact that none of those mysterious clues ever existed. The original reports and documents of the case specifically mention that all the kitchen utensils were clean and there was nothing amiss in the lighthouse apart from two things: a single overturned chair by the kitchen table and the aforementioned set of oilskins. Luckily for us (but unfortunately for the "Aaaargh it was kelpies!" folk), one theory can explain even those: The island was littered with deep but narrow gullies called geos, which could catch water from particularly massive waves and hose it back with extreme force, catching people who were readying themselves for whatever came from the ocean right in the back and expelling them out into the sea.
According to this version, the most experienced lighthouse keeper was attending to his duties in the lighthouse while the two junior ones were securing shit out on the landing stage (which, it turns out, was located right in one of the geos). When he noticed giant waves approaching, he ran out to warn his comrades, leaving his rainwear behind and knocking a chair in his haste. Two guesses as to whether he ventured too close to the waves in his panic.