According to the Wall Street Journal, the drone was taken down with the Marine Air Defense Integrated System. It was apparently the first use of MADIS, which is an anti-drone system that has been adapted for the sea.
MADIS uses jammers to block a drone’s communications which forces it to crash. There are also some versions of the MADIS which are capable of actually firing at drones. The report doesn’t clarify which version of the MADIS was used in this instance.
There has been no confirmation from the Defense Department about the weapon used to take down the drone. However, MADIS was onboad the Boxer at the time. It can be seen on top of a tan vehicle in this handout photo from the U.S. Navy. Iran maintains that all of its drones are present and accounted for and that none have been destroyed by the USS Boxer.