Whaleship not only yields whaleship medals, but also Manyus and occasionally Ampies. And, there's a problem with that. Using those Manyus costs a ton of coins. And the best way to get lots of coins on a daily basis just happens to be.. running the final event mission.
So, my suggestion: do event missions at least often enough to clear your daily (event) quests, so that's ?-1 and ?-2 one time each, ?-3 twice, and ?-4 three times. With the remainder: whale away if you want. And if your maximum stamina happens to be over 300, then do consider using an FG in case you run out of it.

Another thing to consider: how are you doing in the jewelry department? Are all the girls in your main unit(s) equiped with the best jewelry you can get, barring whale missions, or not? If you're still using lots of bronze necklaces and bracelets, then I'd definitely get the event equipment first. Events give you 4 pieces of good equipment for a girl in just 2 weeks. Whaleship gives 1 piece of awesome equipment which still isn't as awesome as a whole set of event equipment combined every other week (that is, if you didn't get any whale equipment yet, if you already collected the previous pieces, then it's one piece of awesome equipment every fourth week).