If you get off the plane and have to change planes in Miami - then you have to go through customs in Miami. It's the first entry point in the US. I had to do it when I was traveling from Europe to New York, and shifted planes to go to Kansas City, also had to do it when I traveled from Kansas City to Australia, with a switch in Hawaii (we had to go through customs in Hawaii) and the same thing happened when I went from Costa Rica to Fort Lauderdale (change planes) to New York. (Do not go through Fort Lauderdale - the worst airport in the US).

If changing planes from Costa Rica to Belize to Miami, you only have to go through costumes in Miama. It's based on the entry point in a country, as you enter it, and if you are traveling domestically within it.