True Sight is not a thing in 4e. There are a few powers that let characters see invisible (a good example being Eyes of the Spider Queen, but it only permits you to see invisible creatures adjacent to you). The earliest level of this that offers a blanket "see invisible" is a level 12 power that requires you be in contact with the earth, which doesn't apply here, and the next best is a level 16 Swordmage power that only lets you see the target of the power, which is hard since the character is flying and out of range of a swordmage.

The lowest level magic item that grants this ability is already a level 3 magic item and can only be used by Shamans, and it only lets them see invisible creatures that are adjacent to their spirit companions.

So spells and magic items are out, that leaves us with: how do we keep the Wizard from flying out and nuking?

Well, a good option has already been recommended: a storm. This creates a challenging encounter for the players on the ship. It also lets you reduce visibility using sea-spray and storm water. It also discourages flight, since i would say it warrants a skill check if the winds are high enough. Reduced visibility reduces the range at which the wizard can cast their spells in the first place, which might be enough to dissuade her, particularily if it brings her within range of the enemies archers and casters, since without a defender around, she's extremely vulnerable to ranged attacks.

This is also one of the reasons I'm not a big fan of DnD... it certainly limits a lot of things.

Quite frankly there should be a standard tactic to deal with any massive exploit like this, otherwise all the wizards would do it.

Broken system is broken.

On that note, there is always the best rule in the book: You're the GM, feel free to cheat when it suits you. Surely give your mage their moment in the spotlight, but if they match certain spells that make them impossible to deal with, just ixnay it with DM magic.

Letting a player do something cool once or twice is fair, letting them disrupt a game for everyone else is flat broken. Why even have an adventure party if you make all the other characters obsolete?

This concept should be a core rule in any game :/

By level 23 in 4e, your characters are at a point where they can start breaking some of the rules of the game ("What was that? You rolled a twenty? Well, actually, it's a 1... sorry") so the fact that they are on a mundane boat in a regular old ocean is already kinda surprising.

The recommendation of a storm doesn't make it impossible, it just makes it challenging, and in in D&D if you can find a way around the challenge, you should be rewarded for it (in this case nuking the BBEGs crew).

Wizards in 4e aren't broken like they were in 3e, where they have a spell for literally any occasion to do anything. They are strictly the Controller role, they deal in wiping out wide swaths of minions (monsters with 1 HP but the defenses of a full monster) and tossing around standard monsters, etc. They need to have a defender around at any level of play, so for the wizard to just fly out to a ship full of enemy monsters to try and nuke them... well, like I said, vulnerable to ranged attacks, and Controllers don't generally have stellar hit points or armor defenses, so storm conditions reducing visibility for the character to be in range of the enemy's ranged attacks makes the exploit possible but extremely dangerous.

DM wise enemy druids are a threat. Swim under your team's ship with their animal companions and warp wood or other nature meddling shenanigans. Also I have been in one where the captain was a druid capable of wild shaping into a kraken or other dangerous beast.

If it fits small parties approaching the ship in row boats to board. Dangers of Cannon ammunition (Ball 'n Chain, Grapeshot, ect.) Bard variants and druids that can meddle with wind and control your parties ship direction and or speed.

Ship battles are difficult and a nice change of pace. Nothing is as chaotic as a ship's deck during battle.(Granted maybe the Chaos realm) It's a good practice in multitasking and in conserving power. Ship voyages are long and perilous so to use all your strength and spells is a big risk for any crew.

You're thinking 3e. Farland is a 4e system. There is no warpwood spell, there are no druid animal companions, the wildshape ability won't let you breath underwater, and NPCs can't have class levels.

That being said, at level 23 the enemy could have a number of allies who can breath underwater and board the PCs ship.

One idea might be to have the PCs make round-to-round acrobatics checks to keep from sliding one or two squares every round.