No doubt about it, the shipping carries the higher number of points.
You have to find the ships before you can attack them. You need an airplane that can deliver some ord that can kill the ship. THEN, the pilot has to score hits on the ship. In order to score hits, you have to get the strike package to where the ships are, while you are defending everything else. With a single exception, ALL of the enemy's bases are VERY close to where ever the ships happen to be found. Other than that, I'd say go for the ships.