Ran into a similar situation in Panama last year (and have in many other venues in the past). The officials were quite easy to work with in our case...went out of their way to help in fact.
Having a letter from captain/owner (and maybe even a copy of the Ship's cruising permit) will definitely make this go smoother.
If the captain/owner is able to meet you at the airport
that is not a bad idea either. I've resolved some issues in the past with crew/guests flying in just because I was there...not sure how it would have gone if I had been absent.
The issue may not even come up at all, but I still suggest being prepared just in case. I've had officials not even bring it up before (but that was back in less security
conscious times). Being prepared sure beats being sent back home -- and I've seen that happen too.
Oh, and be nice. Treating officials with courtesy, patience, and respect goes a long way. They will probably respond in kind.