Kasey,
I'm assuming the leaks are on shore or else you would have seen the bubbles coming up where they shouldn't. If it is a shore-based problem then PVC will work as mentioned or you could simply bury your line. Take my word for it, sheathing feeder tubing with PVC is not as simple as you might think, especially over long lengths and if the problem is in the water. My partner and I sheathed about 1000 feet of feeder tubing (in water) with 1.5" PVC to avoid beaver damage in one pond. The install, although successful, was a total pain in the butt and took twice as long because of this. If you do go the PVC route, you would probably only have to do it around the shore where they are most active which wouldn't be too bad.
You could also try altering their habitat. I hear that lowering and raising the water depth frequently will drive them off. Also, keeping the vegetation trim around the pond will reduce cover and will not be as inviting to them. I don't like this as much because the tall vegetation acts as a sediment trap and attracts insects that your fish might like to eat. You could also try eliminating their food source but again this would involve removing vegetation...although, cattails can be a staple of their diet which most pond owners are happy to reduce or remove.
I've already rambled too much. There are resources online including this one
http://wdfw.wa.gov/wlm/living/muskrats.pdf which offers some management techniques. Good luck.
