The only way I could get it to lock on was destroying all 4 of the gun turrets.
2 Rocket hits, or 3 Gauss Rifle hits to each one.
Then they finally said alright lets move in and deactivate the shields.
After that they will tell you to lock onto it.(left side first)
Take out the Tactical Nuke Gun, aim it at the left pod.
After about 5 seconds it will have locked on.(try not to die from the aliens attacking you)
Once that Pod is down you must survive until they deactivate the shield on the right side.
Once that is done, repeat the steps that you did on the left Pod.
Alien Warship get angry now!
Make sure you run and get more Gauss Rifle ammo or Rockets.
Staying cloaked during this time helps to get in position.
Fire 3 or 4 rockets/Gauss Rifle shots into the door that opens underneath the ship.
THEN RUN TO THE FAR SIDE OF THE CARRIER BEFORE THE WARSHIP SINKS THE BOAT!
Super Speed always helps at this point.
Enjoy the ending credits