Use a tamed sea serpent. Build a Serpent depot on the water at each harbour, ride the serpent to the first depot and press Record route, then ride to the second (up to 3,000 m away) and press Finish route there. Click chests within 30 m of each depot with the wand to set pick-up and drop-off chests, then switch the serpent to cargo. It sails back and forth on its own. If the far shore is within 200 m, a pair of Haulwright relays also works, because Haulwrights fly.