All of the Transport maps are extremely simular and everything I say to help you through one applies just as much to the others, so I'm only covering one. In Transport Harbor, you start in a container.
The base idea behind all 5 Transport missions is there are 1-4 Transports pulled over and you need to get inside them and take whatever is in them. You can either drill through the doors or blast them open.
Using C4 is was faster, but it blows a small amount of the loot up as well of the doors. If you want all the loot and don't mind waiting, Drills are the only way to go.
Once you get inside the van, you're greeted with a lot of Deposit boxes. Yay. You can either SLOWLY pick the boxes open one by one, or bring the Saw and tear through them. It's not recommended to bring the saw if you plan to be drilling the doors open especially on harder difficulties, because you're left with only your secondary weapon for the period of the drill.
In the deposit boxes you'll find a certain type of Baggable loot, along with dud items and loose loot. The bags can be anything from Jewellery to Money to Gold.
As soon as you bag one piece of loot, the Loot Van/Boat will start on its way to you. Grab all the bags and hold up tight in wait, or leave the unbagged loot in the trucks so the cops can't steal them.
When the boat/van finally arrives, move the bags from the holding spot (or bag from the trucks) and throw them in and escape.