I agree that Charlottesville checks all the boxes. A few smaller, more off-the-radar picks:
Davis, WV: abundant trails, real mountains, ~3hr from Pittsburgh. Local outdoor scene is good, but can't speak to running community specifically.
Marietta, OH: Sleeper pick. Great urban singletrack network (20+ mi of trail and growing), plus hundreds of miles of trail in the nearby Wayne National Forest. Within 2-3 hours of Columbus, Pittsburgh, and Cleveland. Terrain is very hilly, but you'd have to drive to ~3hr to get to real mountains in WV. Local running scene is small.
Saranac Lake, NY: Close the Adirondack High Peaks, great access to trails, surrounded by beautiful lakes, but more of a "real town" (has a hospital, not all properties are rentals or second homes) as opposed to nearby tourist destinations like Lake Placid and Keene Valley.
Others: Burlington and Waterbury, VT, Greenville, SC, Harrisonburg, VA.