Penguin's ship [Final Offer] is moored in the North-Eastern corner of the map, i.e. to the East of The Amusement Mile. I recommend that you approach the ship from the South-Western side, especially that the area is being observed by two snipers and it would be a good thing to eliminate them quietly. The first one of the snipers is occupying the mast shown in the above screenshot. Glide down towards that person, walk him from behind and perform the silent takedown.
The other one of the snipers is deployed to the North of here. Use the option to glide and the hook to get to the red container hung down, and then to the crane. Eventually, you need to reach the ledge directly above the sniper in question (the above screenshot). Land onto the sniper and stun him before he regains his strengths.
Note! Do not walk away from the area guarded by the enemies, because they can quickly respawn. This is true also for the two snipers that you have just eliminated.
Although the threat from snipers has been eliminated, I would recommend that you also eliminate the remaining enemies by operating from shadows. This is so, because they are equipped with firearms. First of all, focus on the two guards deployed to the right of the place where you have taken down the second one of the snipers. Land behind one of the gangsters, attack him by surprise and eliminate the other one in the same way. Note - if you are spotted while clearing the area, you can leave the ship's board, grapple onto one of the cranes hide in one of the small tunnels.
On the opposite side, there are three guards and, since two of them stay put in one spot, eliminating them will be a bit easier. I recommend that you eliminate the enemies in the order presented in the above screenshot so, by starting with the one patrolling the small, central, bridge (only after he stops near the two other enemies).
Finally, you need to deal with the two enemies that guard the door below. They are occupying one spot each, which makes it impossible to attack them from above and, apart from eliminating either of them would alarm the other. That is why, it is a way better idea to encourage them to leave their posts. If you have only the standard gadgets, hit one of the guards with a batarang, and hide quickly. If you, on the other hand, have already gained access to some better elements of the equipment, consider using the Sonic Batarang.
Regardless of what you choose to do, the enemies should, eventually, leave their default positions. In theory, you could attempt to reach the exit straight away but, since the enemies should pretty quickly separate, it is a better option to eliminate them with effective surprise attacks. After you have dealt with all the business here, take the door to the ship's deck.