Railgun Fighters do well against those, give 'em 10cm Railguns with Capacitor 3, Railgun Launch Velocity 20,000 km or better and pair them with an FCS that has at least 20,000 km range... and that is the bare minimum.
30,000 km Launch Velocity and 60,000 km FCS Max Range is much more comfortable, while 20,000 km Launch Velocity and 40,000 km FCS Max Range is cost-effective. Make sure that the FCS tracking speed is matched to the fighter's own top speed if that speed exceeds your base FCS Tracking Speed, i.e. the Tracking Speed that your Beam FCS has before changing the Tracking Speed in the Component Design window.
Also, make sure all of your PD Fighters have at least a small Res 1 Active Sensor. An additional fighter dedicated to sensors is very helpful, but it is wise to ensure that it's destruction does not result in a mission kill for the entire escort formation. Of note, you could also create a bomber with AMM "Canisters" by adding some extra Box Launchers dedicated to holding a missile stage comprised of nothing but AMMs set to deploy immediately upon launch. A 20 Ton Res 1 Active Sensor and a 5 Ton Res 1 Missile FCS make a good pairing for each bomber, so when you detect the missiles, you can launch the AMMs.
Consider using 2-3 layers of armor, depending on your tech; it makes them that much harder to shoot down. A Small Craft ECM 1 module is nice to have as well, gives you a 10% evasion against missiles that lack ECCM, which is a common trait of typical AMMs as they tend to work best as cheap, high speed, high agility spam missiles.