I had a hell of a time with this section, but finally beat it by:
1. Set the bomb in the front and IMMEDIATELY jump overboard and swim like hell for the shore. You prolly won't make it to shore, but if you're healthed up (check the wheelhouse) and almost onshore, the damage from the explosion is survivable.
2. As the chopper circles around, use the palm tree trunks as cover and when there are breaks in the chopper's firing, pop out and hit him with the rocket launcher. It takes 6-8 hits IIRC to down him, but it's easy to nickle and dime him this way.
The trees are better than the ship's structure because it's easier to circle around into cover, the canopy provides a screen and all shots only have to worrt about lateral movement and not vertical.
Hope this helps - it only took me 2 tries this way.