I would let the rope trick ride with the boat. I'd imply an anchor spot outside the rope trick, being the five foot square of ground where the end of the rope hangs, as anchoring the spell to that space. I feel it is implied when the spell states: "one end of the rope rises into the air until the whole rope hangs perpendicular to the ground". "The ground" in this case is one end of the anchor (with the window being the other). If that end of the anchor is moving, in this case if the "ground" is moving, then the location of the window changes, since the location of the window is defined by and related to the location of the ground (5' to 30' away from the ground, depending on the rope length you chose when casting the spell).