In the last level plutonium runs loose I get on the ship easily but I can..

He's hiding on the middle level of the ship, at the north end. From the center bridge of the cargo hold, head north until the gangway splits up into two. However, both paths are guarded, and if you take one out, the rest of the ship will be after you.

I find it much easier to take out all the guards near the entrance of the ship, and then go to the stairs leading onto the ship and shoot one or two guards from there. They will alert Boris, and he will arm the nuke before fleeing the ship. Just stand at the bottom of the stairs with an automatic weapon, and shoot them as they leave the ship. There'll be Boris, Ivan, and two or three guards. After they're dead you can board the ship to disarm the nuke.