The easiest way to stop a drone attack against the U.S. would be an EMP (Electromagnetic Pulse)

However, the real problem with this is it also might cause jets to crash and all GPS devices to stop working on the ground. But, rather than hundreds of thousands of Americans dying from little hand grenades being dropped out of thousands of small drones this might be one option. The other problem with an EMP is wherever it hit would be that all hard drives on computers in that area would be wiped clean too. But, I think it likely is better to save lives by doing this anyway if a large 100 to 1000 or more drones attacked against the U.S. mainland all at once.