I actually had to hear this from my daughter, so I'm probably not the best person to explain it. But basically an anime (School Days, I think?) was supposed to end with a horrific murder committed on a boat. (It was based on a game and that was one of the bad endings.) But there had been a horrific murder in real life that was similar in some ways, so they decided not to air the ending. But rather than just not show the whole episode they cut that part out and showed live action footage of a boat just kind of ... sailing around.

And "Nice Boat" thus became a meme.