I think word of mouth from the locals is the best way to pick, they'll tell you who is a crook, who is fair, who for warranty work, who for this brand or for that brand.
For instance around the Raystown, Shy Beaver Boats for Mercury dealer service and warranty good but pricey, Jims Anchorage had 30 somes years with OMC til the end and is with Bombadier now, they are very good with Johnson/Evinrude but also a bit pricey. For an independent guy and good all around service I would go to Mike at Arnold's Marine, he's a good mechanic, easy to talk to and fairly priced. I won't call out bad guys, but I've dealt with about all of them from Saxton to Huntingdon and I would not go anyplace I didn't mention here.