If I'm not mistaken, you're probably talking about the mission called "The Made Man" when JD gets killed.
Dude, what you have to do after driving Mickey to his house, is to check the map to see a nearby spot where see is located. From where you are, if I remember right, you have to go reverse and then turn to the left. The see whould be further in front of you. Keep gaining speed and when you're near the edge, press the triangle button to bail out of the car, which should then drop into the water, thus making this mission passed.
Sorry if the above confuses you; it's kinda late and my mind's not working properly. If you can't still get it, I recommend you see a FAQ/walkthrough at GameFAQs. Good luck, buddy!