How.. how do I get off of a Enemy Flagship?

[Steely Jim]

Look for a gap toward the rear of the port/left side of the ship. Keep trying to jump down into that gap (keep trying, and switching directions and jumping). You should be able to swim back to your ship. I use a war sloop and was able to jump back on board my ship, and after a few came over to my ship, it eventually let me swing out of the encounter (even though I was already back on my own ship).

EDIT: You should have a second or two before the next wave respawns; that's the best time to try jumping out through that gap.