Shipping goods on an empty vessel in Puerto Rico
Keep in mind that shipping takes place in several turns, going around the table starting with the player that chose Captain. On your turn, you must load a good if you are able. This means that you could choose to load all your indigo on the empty ship (provided that the third ship is not already carrying indigo--there can be only one ship carrying each kind of good), or you could load as much of your corn as you can onto the half-full corn ship. On your next turn, once each other player has had an opportunity to load, you must load the other good, if possible. Only once all allowable loading has finished and all players have passed does the Captain phase end.

If, for some reason, you wanted to not ship the corn, you would have to ship the indigo and hope that another player filled up the corn ship on their next opportunity. This happens more frequently when you have an expensive good like coffee or tobacco that you are hoping to trade rather than ship.

A couple points, summarized from the rulebook (p. 6)


Each ship can only hold one kind of good.
There can be only one ship of each kind.
On your turn, if you have any loadable goods (with a legal space on any ship) you must choose one of those goods and load as much of it as possible. However, you are under no obligation to make the choice that will load the most barrels.
If you have a choice of multiple empty ships, and enough of the good you are shipping to more than fill up the smallest, you must choose a ship that is large enough to load all the goods, if you can, or the largest empty ship otherwise.
You are not obligated to use a wharf to ship if you happen to own one. (p. 9)