We recently discovered we have squirrels in our attic. How much would your average cost be for a medium-sized?

You need to call a licensed animal removal specialist in your area. No way to tell you the cost on here since such services vary widely depending on where you live (I am a construction estimator and that is true for ALL services.) If you can't find one on-line or in the phone book contact your municipal animal or pest control department and ask them to recommend someone. The house will have to be sealed up whereever they are getting in (usually under the eaves or at broken masonry around chimneys.) Most removal services can provide cleanup and reinsulation but you will probably want to get it fumigated: squirrels are notoriously covered with fleas. You might want to check your home insurance coverage to see if any of the repairs and remediation are covered by your policy.