Don't really have an answer for you - but have you thought about doing a B2B? We want to do Tahiti, but are waiting until we have a little more time in our schedules.
Like you, we are interested in Cook and Marquesa Islands. Thought this might be the best answer.
First of all you need to look into the Air New Zealand schedules as they are the airline that flies between Papeete and the Cook Islands.
I know they only fly certain days of the week and then I think it is very early in the morning. Saying that, your return back to Papeete may easily be on a different day so that you could miss the ship.
When we flew in to Papeete we flew via the Cook Islands and that was on a Friday arrriving around midnight but when we were returning home, we flew out on a Friday morning at 5am and our flight was direct to Auckland.
Until we sail on the Tahitan Princess - Tahiti to Hawaii
Until we sail on the Nautica - HongKong to Athens