There are three big aircraft carriers (huge ships) on this stage, there is a Chao Container on each one!
Chao Container #1
On the first aircraft carrier, the Chao Container is tucked in the corner next to some large storage garages, just before the part where you have to break some steel boxes to fly off the ship.
Chao Container #2
On the next ship, the Chao Container is next to some large cylinder fuel tanks near to where the large amount of inactive G.U.N. robots are being stored.
Chao Container #3
On the final aircraft carrier at the end of the ship, the Chao Container is again next to some large cylinder fuel tanks in the far right corner, hidden behind a single steel box.