There are probably an infinite number of ways of doing this. And any of these ways will be the best for its specific situation.
In spite of that I am going to address a few rather broad concepts based on different mechanisms and indicators:
A) Give them an overview of their situation
Depending on how open your level/world is, you have different ways to do this.
An obvious and easy way would be to provide a room they have to pass through on their journey which gives them an overview of the area.
This could be e.g.:
The Bridge of your ship; A room that is central to the vessel, situated on top of it and offering a panoramic view of the upper decks. Add visual indicators like runway lights for the seaplane catapult (or whatever you use to launch it) or e.g. lights recessed into the floors, leading to the emergency rafts. Or even go plain aggressive and light these things up with floodlights.
The Security Room; A room in the bowels of the vessel, full of TV screens that are displaying the views from different cameras all over the ship. You can make some of these screens stand out by making them brighter, turn other screens off, show people running along hallways towards something, etc.
Maps & Escape Route Signaling; Add maps and signs to thoroughfares and cross-ways that indicate important areas you want the player to be aware of. E.g. add signs pointing towards The Seaplane Hangar or Starboard/Port Lifeboats.
B) Force them to make a decision
If you're willing to restrict the player in their movements to some extent you can present them with a situation where they have to make a decision: Go either left or right, up or down, etc.
You can make them aware that they've made a decision by adding different less and more obvious cues to the mix. E.g. remove the signs pointing towards the other option, add a radio transmission or a scene of someone using the other option to escape themselves, etc.
C) Show them possible alternatives
In the spirit of forcing them to make a decision you can also show them that there's other ways to achieve the same goal.
For example, you could design your level that by choosing one path, you will eventually move along a path that leads you past the other option, showing it maybe behind a chain-linked-fence or a window - unattainable but still there. Maybe adding some animations, again of the other solution being used by an NPC.
While eventually escaping you could show someone using the other option, e.g. the seaplane flying over the character sitting in the life-raft.
You could add cues to the next map, e.g. a radio-log of someone asking if anyone made it off the ship using the plane/boat/etc.
Now, all of these have obvious advantages and flaws. It is up to you to find out which works best for your map/scene. You will also see that your planned audience will influence your decisions in a major way.
While some people are of the curious kind, wanting to find out if there's other ways. Others will already be satisfied by having made it off the ship, and will never even spend a thought on there having been possible other ways.
An example of this is the opening sequence of Skyrim. There's a very first decision in the game right after the dragon's attack, but I doubt that most people have ever become aware of it, even now.
The decision is to either go with the stormcloaks or the empire. And while it ultimately doesn't really matter, it still changes the early game by some extent - shoving you off onto different factions and slightly different initial questlines.