The phrase you're looking for is "American company". Apple is an American company.Apple is ultimately a U.S.-based company that has to play by the rules of the nation (even if they are only temporary executive orders).
No one would say "Japan based company". They would simply say Japanese company. It is strange to me that everyone likes to pretend that nothing can be American. Or maybe it makes them insecure to knowledge that most of everything that matters in tech is American.