The following options were recommended by a local runner:
the Wehle State Park near Henderson NY has excellent trails along cliffs overlooking Lake Ontario; the “ocean-like” Lake Ontario beach at Black Pond Wild Life Management Area;
the cross country trails at Thompson Park in Watertown and behind Watertown High School and the Black River 7 mile trail on an old railroad bed – hard packed.
Also take a look at Northernrunner.org for area races and there is a list of walking running trails at http://www.trailjeffersoncounty.com.