I figured that when they said "boat" in the movie, they were referring to the freighter/transport vessel that Nedry tried to reach at the beginning of the game. "That's up to your guy on the boat" etc..., not some mysterious speedboat docked on the other side of the island.
In fact the game makes no mention of the speedboat until they show up at the docks and voila, there it is. They could've at least inserted a bit of dialogue for Nima or Miles at the beginning that alluded to it.
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