It doesn't have to come in in a cargo container either.
Sailboats in the 35-foot & above class routinely cross both the Atlantic and Pacific. There are a lot more of these than most people think.
I can think of numerous ways for a boat of this class to smuggle 1000-2000 pounds in the US.
Most ports of any size are also patrolled by Coast Guard vessels, which all have active radiological scanning function.
Unless your target is very small, you'll never get near enough to hit anything.
"I can think of numerous ways for a boat of this class to smuggle 1000-2000 pounds in the US."
Exactimundo! Which makes me believe that the bad guys don't have such a weapon...yet. If they did, they'd have used it by now.
There's really no way to completely keep out such a weapon, that is the scary part.