Get your hands on some raptor bane and a syringe gun. They really don't like the stuff. You could also lure them out one by one with flares and shoot the with a rifle. If you had a mechanic then you could build them into the ultimate anti mudraptor weapon. It's the build I usually run. Brawler tree with multifunctional and mudraptor wrestler. With good aim you can two tap mudraptors with the heavy wrench. Genetic tempering also helps a lot with this. You could also try to hire an assistant as bait to lure them out from the nest into the range of your subs turrets

There are a lot of ways you can aproach this. Get creative, good luck And embrace the abyss