Pittsburgh Bottleshop Cafe
Church Brew Works
Fox & Hound
I'm sure there's a lot more - please chime in!
Also, there's a place between Pittsburgh and Erie called Sprague Farms. We were visiting my father in law who lives out that way and when we were waiting at the bar of a restaurant for our table, I ordered a local beer. It was delicious and the bartender told us about the 'brewery'. We went to visit the next day, and it was about the coolest place i've been. It's in the middle of nowhere, and it's just this guy and his wife who bought a farm and turned it into a brew pub. We had such a good time that we rented their spare farmhouse with a dozen friends and had my birthday party up there.
For the record, I'm not affiliated with them at all - just a big fan. Their website is www.sleepingchainsaw.com