Atop the ladder near the lift leading to the crane. Or, from the big fan room its either right in your path or on your left through an opening depending on what path you took.

If you used the sewers to reach the ship, you'll earn this just before you hit the water. (Secret hand sign to The Burdman for the tip.)

Enter the crane control room.

On the north (port) side of the ship are three means of climbing aboard. Two ladders, bow and stern, each will earn the points about 3/4 of the way up. Near the ladder towards the the bow is a crane hook. It can be climbed. When you reach the top, walk about halfway down the crane arm to earn the points. All three of these are earnable, earning one does not cancel the others.

Aboard the ship, get to the bow (front) by jumping atop the edge and carefully walking atop it. At the bow, head to the crate and GEP Gun to earn the points.

Exit out the top starboard (right) side of the ship. The hatch is unlocked and is south of the bridge.

Enter the mid-deck of the ship through either side hatch.

Enter the captains quarters on the topmost deck.

Make it to the below decks part of the ship. The locked hatch at the bottom leading to the next map.
 

For every tri-hull weld you destroy you get 120 points. 600 total when you blown all five.

After raising the bridge in engineering, you get these points when you reach the room by accessed by crossing the bridge.

In the room with the large fan you can float up on the air stream. At the top are two vent shafts. Entering either one earns the points. Double, of course, if you enter both.

In the southeast corner of the bilge pump room is a platform with a crate. Access it by crawling through the vents or carefully jumping across the bilge pump while it is in motion.

Enter the control room overlooking the helipad. Several ways of enter this control room include a ladder inside the helipad area or disabling the electricity near one of the tri-hull welds to safely cross the catwalk leading to it directly.

Use the vents in the electrical generator room, west of the helipad, to access the helipad. You'll pop up in the helipad towards the back near the base of the pad itself.

Climb atop the helipad and run into the attack helicopter. (Thanks to The Burdman for the info.)

Explore the grave of Bill Iberg. Can also be accessed by one of the tombs inside Dowd's crypt.

Enter the open grave northeast of the cemetery entrance. Go all the way down to the alternate entrance for Dowd's crypt.

Talk with Stanton Dowd in his crypt.

Destroy the EM disruption generator behind the bookcase inside the gate keeper's shack.