Choosing the Best Approach : The Merryweather Heist : GTA V Guide : XBOX 360 PS3 PC
Whichever approach you choose the outcome of the mission will be the same.
The freighter approach involves some sniping and putting bombs all over the freighter. A little later you have to drive a submarine to pick up an item.
The offshore approach involves flying a submarine to the ocean with a helicopter and picking up an item with the submarine. You will also have to defend the helicopter from some enemies.