I've heard that keeping the grass trim around the pond will eliminate some of their habitat and annoy them enough to leave.
Also, according to the Illinois Department of Conservation in Fisheries Bulletin #5 they state:
"muskrats may be trapped during the open season, or they may be driven from the dam area by drilling holes at 3-4 foot intervals on the upstream face of the dam about two feet back from the waters edge. Extend the holes about two feet below the water line. Place four to five ounces of creosote, calcium carbide, or napthalene in each hole and fill the holes with dirt or sod. When a digging muskrat comes in contact with the treated area, he will usually leave the area."
Sorry I don't have an e-link, this is just an old document we have laying around the office. Muskrats can wreak havoc on aeration tubing. This document also suggests flucuating the water level by 1-2 feet every 3-4 weeks until they leave.
One final kind of humurous suggestion from a different document put out by the Dept. of Interior and USFS (1983) is frightening them, and I quote, "gunfire will frighten muskrats,
especially those that get hit, but is not effective in scaring the animals away from a location." I suppose that in this case you have to pick the dead ones off the shore and dispose of them in order to get them to leave the area
.