Consider using the Deuce. Either the regular missiles or the heat seekers should be able to take them down pretty quickly. The key is getting their attention so they start charging you, otherwise it's hard to concentrate fire on them if they're running around the battlefield.
Once they start heading your way, simply back up and keep firing, and if they get too close, the side-mounted subwoofers can stun them for a few seconds.
This works equally well against lone Reapers you encounter in free-roam mode.