Carlos Rafael seemed like an all-American success story. A Portuguese immigrant, he started out cutting fish on the dock in New Bedford, Mass., one of the most important fishing towns in the world ever since the days of Moby Dick. Over the years, Rafael, now 65, put together one of the largest commercial fishing fleets in the U.S., with almost two dozen boats, controlling almost a quarter of New England’s landings of groundfish and scallops. But now he’s in jail, having pleaded guilty to conspiracy, tax evasion, smuggling cash and falsifying his records. And the boats in his fleet, which…