Lucky Dog Cafe in Confluence is quite good. Their menu lists vegetarian dishes, but not vegan. I've had "Vegetarian Black Bean Burger - Topped with Monterrey Jack cheese, avocado, lettuce & tomato served on a brioche bun" and it was quite good. The restaurant is about 200 feet from the GAP trail, where it crosses the Youghiogheny River.
http://www.yelp.com/biz/lucky-dog-cafe-confluence
If continuing on to the C&O Canal Towpath, try the Desert Rose Cafe in Williamsport:
http://www.desertrosecafeandcatering.com/ . Veg options - yes; vegan - maybe.