I'd say it all depends an you, your crew, your co-captain, the four ships, the map and, especially, the situation.
There are gunners that can destroy a mortar quickly with a gatling and there are gunners that can't destroy a hwacha with a field gun. It depends on how good your engineers are, what ship you and your teammate are flying, how you are at which map targeting at how many of which enemy ships ... there are just too many parameters to simplify that.
There are only few situations in which I have to tell my gunners what to aim for, mainly you can go with a straight takedown. I generally like the enemies guns destroyed as fast as possible. Same with the balloon, which I like it to be destroyed at the same time as the hull/guns. Engines ... well, only effective against fast or maneuverable ships or in special constellations.