The USN has been doing a lot of research as to the best methods of stopping a swarm attack. And as is typical, they are very tight lipped about it. However, known area weapons could already reduce such a fast attack boat “armada” to flotsam.
For example, a propane bomb. Typically helicopter dropped, when deployed, it spins while spraying out a large cloud of propane, which it then ignites. Used on land, this causes a jump in atmospheric pressure from 1 atmosphere, to about 4 or 5 atmospheres in less than a second over an about mile square area. With very lethal consequences for those within its range.
Since water does not compress, over water it would be much worse.
An example of this is the CBU-72.
https://en.wikipedia.org/wiki/CBU-72
Cluster bombs were my first thought as well. But the discouraging thing is that the last line in the Wikipedia citation you provided indicates that our remaining CBU-72’s are being “demilitarized”, which I take as Obama-speak for unilateral disarmament.