Fortunately for you, we're better at speculation than that. The Keepers of Time in front of the portal say the ship is a "Kaldorei vessel," which points directly to the Night Elves. Now, the Night Elves are not exactly a seagoing civilization, but there is one time in which lots of them perished at sea, and that's during the War of the Ancients and the ensuing fight over the Well of Eternity. I'll let Elizabeth give you the details in one of her great Know Your Lore features, but suffice it to say that Malfurion Stormrage (the greatest druid ever and Illidan's brother) stormed the old continent of Kalimdor to fight against the insane Aszhara and close the Well for good. In the process, the Well of Eternity was destroyed, Illidan did some evil stuff and escaped away, and lots of elves drowned (in fact, some of them became the Naga, and the Well itself became what we know of as the Maelstrom). So while we're not sure exactly what event the portal revolves around, it very well could be somewhere in there-- either fighting alongside Malfurion, helping Illidan escape (so we can fight him in the Black Temple), or helping the Kaldorei find their way out of the war to their current stomping grounds.
Still other guesses from players (about this and other upcoming instances in CoT) have to do with Illidan's treachery (any of it), the Theramore invasion fleet, or even a visit to the past of the Deadmines (lots of players want to see a pirate instance, I guess). Of course, there's always the chance that the Instance is just a placeholder, and that the boat is a red herring. Either way, Blizz has made it clear that the CoT is going to see a lot more action, wherever (and whenever) it takes place.