I've heard something about an irregular ferry across the Gulf of Fonseca, leaving La Union, El Salvador, and arriving Puerto Potosi, Nica. This story
is six years old, so take it with a grain of salt. If you are trying to save time and money, I don't think a ferry is your best bet here. Land border crossings aren't particularly painful, whereas port procedures, especially in out-of-the-way places like La Union, are more tedious. If you do it by bus, you might get hit for a dollar or two mordura at the border, but it's not a big deal (and since this ferry crossing is obscure, you'll probably need to pay a bigger bribe if you do it that way). I've never had to spend more than 20-30 minutes with border formalities in Central America at a land crossing.