A Meme that originated from 4chan, which then cross-pollinated to 2channel and the Japanese internet community.
It originated from the anime School Days when several broadcasters refused to air the final episode, considering it inappropriate due to a recent event of a girl murdering her father with an axe.
One station in particular, TV Kanagawa, aired a scenic nature program instead. One of the scenes in this program featured a boat on a lake, hence the phrase "nice boat". The phrase didn't really take off as a meme until the last episode aired, with it ending... on a nice boat.