Not entirely sure which one is which to be honest but I'm guessing its the one on the long skinny island. If its that one the island I mean is the one where you find Pedro. It's also the one that has the two wooden bridges that you destroy during the boat chase section. From those two bridges if you just fly right down the middle of that island it's quite close to those bridges almost smack dab right in the middle of the island. Fly SLOW in that area and you should see the lights blink eventually. Look for this one BEFORE destroying the radar station. That point isn't timed so you have plenty of time to fly over that island to look for it.
If its the other one that's even easier. AS SOON as you get control of the copter immediately following destroying the cocoa fields don't fly anywhere. Just turn to the right and same as above, fly slow or hover until you see the lights on the crate blink.
Well I get up in the morning and I get my brief. I go out and stare at the world in complete disbelief. It's not righteous indignation that makes me complain. It's the fact that I always have to explain. - Van Morrison