Take out the Dust Men on the roof directly across the street, then climb the building they were on. Move quickly before more Dust Men flood the street. Avoid placing yourself in sight of the gun turrets to the sides of that building.
From the roof, take out the Dust Men and board the first ship. Go to the back and zap the engine and free the prisoners. Go swiftly west to the second boat. Resist the temptation to ride the rails; you will come under heavy fire if you do. Go across the buildings on the opposite side of the tracks until you are opposite the pier. If you approached quietly enough, you will not stir up the Dust Men on the pier and you can glide across to the roof of the warehouse and take them down from there. Otherwise, you have a nice vantage point from the opposite side of the tracks to lob Grenades and Hammers at them.
Once again, free the hostages and zap the engine. Now ride the rails counterclockwise to quickly reach the third pier. When you reach the train station right before the pier, stop and take care of any Dust Men that spawn in the station. The tracks are covered by machine guns on the roof of the warehouse, so take them out (Hammer or Precision) before going any further.
With the turrets quiet, you can jump to the roof of the warehouse and deal with any opposition on the ground. Then, get on the ship and disable the engine and free the hostages.
There's another boat and it's clear on the other side of the district. The shortest route takes you through a dark area, but the other way is just too long to take the train. Either ride the rails counterclockwise or go over the rooftops. There's a machine gun in the dark area of the tracks, but you can get through if you just keep moving.
There's no easy way to do this. Your approach to the fourth pier has to be out in the open. So make sure you have plenty of energy for Hammers to throw at the RPGs on the roof of the warehouse. Shockwave any rockets that get thrown at you and try to knock the Dust Men off the warehouse as quickly as possible. This is really it, so free the hostages and then destroy the engine to end the mission.