In BOA, the French Indians of Montcalm's scenario play a very similiar role of raiding throughout the American colonies. My counter is to use patrolling garrisons.
Typically I will have one or two militia regiments forming garrisons at each major strategic city. But they are not static garrisons. Each garrison is responsible for constantly patrolling the regions around their strategic point. The route of patrols focuses on the more likely approach routes of Indian bands.
Even against a human player, my patrolling garrisons will bump into those unseen raiding Indian bands and neutralize them-usually in terms of casualties but also in terms of ammo supply reduction. Raiding parties, in BOA, cannot resupply without a friendly base. Being in friendly territory, your garrisions can quickly refit from losses as well as resupply ammo.
Usually my patrols will win the battle against small Indian bands. But even if your patrolling militia loses the battle against a larger Indian band, the Indians now have a much higher risk if they wish to continue the raid due to casualties and ammo losses. A second battle just might wipe out the Indian bands and a completely wiped out Indian band is usually an unacceptable risk. Regardless you now have a location to direct reinforcements against a weakened enemy.
I don't know if the patrolling garrisons would work in ACW but works very well in BOA.