After finishing Scouting the Port, play as Trevor and you will eventually get a text from Wade mentioning he saw a sub, which will put a new mission marker on your map. Head to the docks and find the ladder to get onto the ship. Note that there is one guard who patrols the ship, so if he sees you, then you will end up with a wanted level.
To free the submersible from its restraints, there is a button that is marked as green on your radar. Press this and the sub will fall into the waters below. Jump into the water, climb onto the top of the sub and then enter inside like any other vehicle. If the cops are after you, simply go underwater until the stars disappear.
Once any stars are gone, drive the sub to the marker on your radar, where Floyd will use a crane to place it onto a truck. When you're in the truck, drive it to the warehouse to finish the mission.