The visitor center is placed along the most aesthetically pleasing coast, with a nice sandy beachfront for guests to enjoy. A oceanfront view that's 0 beach and obscured by jungle does not a Grade A theme park make! The location of the Loading Dock would have been selected purely for logistical reasons. Not any random stretch of coast can be turned into a harbor, and making an artificial one or even dredging a pre-existing shallow harbor can be wildly expensive. Cargo ships need quite a bit of depth to maneuver safely, and as such they likely just took the best deepwater harbor location they could find. (after all, Hammond's "spare no expense" doesn't seem to extent to, you know, things that make the park safe/efficient, just sexy.) Given the small size of the island the location doesn't matter too much, so InGen probably just used the best natural harbor on the island for the supply dock, and picked the location with the prettiest view for the Visitor Center.
The helipad is harder to fathom, but ostensibly they might want it far enough away from the Visitor center that the noise of choppers flying in/out doesn't disturb the guests' experience. (either visually or via noise pollution) If you want it out of the way, don't want it actually in the mountains (expensive, potentially dangerous in case of emergency), but also want to maintain as much grasslands as possible for your dinosaurs, the helipad's location is the only one that would let you make a road to the visitor center without making one through mountains (which again would be much more expensive). I can't swear they want to keep all the grassland for dinos, but given the only light-green area NOT part of a dino preserve is a bit right next to the visitor center it seems like a safe bet.