You need to talk to the sailor at the end of the dock in Ibanna Port; all the way east of the map on the southern most street.
It's tricky to get to the sailor because of all the people standing in front of him. Use your keyboard to move the character, walk all the way to the south edge of the dock, your character will be partly covered with the dock's fence, and then navigate your character through the people standing there until you can talk to the sailor.
He will tell you the boat will arrive shortly, you have two options: "We will wait here for the boat to arrive", or "We are not ready yet". I don't remember the exact words or order of these two, but that's the gist of it. Choose the one that says you'll wait there, and you'll be on the boat heading to the Imperial City port in no time.