When I was in Vermont a few months back, we went to Long Trail brewery which has a self-guided tour, but sadly you can't fill growlers there (but they do sell six-packs). It's an okay tour if you're in the area, but in retrospect I wouldn't have gone out of my way as much as we did had I known.
Regarding Pennsylvania breweries, if you're in Harrisburg anyway, definitely try Troeg's (they only offer tours on Saturdays though if that's an issue, but at least check out their brews. They always have something interesting on tap with their "scratch" brews).
Appalachian wasn't very impressive to me, but they do have excellent food and a few good brews, which Troeg's only has snack food. If you're looking for lunch while in the area, it's a good stopping point, I just wasn't too impressed by the tour.
As others have mentioned, Bube's is pretty close if you're in the area, and is worth checking out. There are a handful of other breweries in that region of Pennsylvania, but outside of those mentioned above, if you find yourself near Philadelphia-area, Victory is definitely a good one to check out. Great selection of food, beer and a decent tour last I was on it (but they have expanded since).
In Philadelphia itself there are some good breweries such as Yards, which has a fun tour and is a great place to hang out. They have lite fair for the most part, so if you're looking for a more brew-pub experience, I'd check out Nodding Head Brewery (
www.noddinghead.com) which has a nice Berlinerweisse from time to time, as well as many other interesting brews. There is also a Triumph Brewery in Philadelphia that is decent, and there is always Philadelphia Brewing Company which has a few decent brews. There's plenty of breweries throughout Pennsylvania; there's a book of the various breweries but I've not even touched them all yet!
Sounds like you'll have a fun trip regardless, but hopefully from some of the feedback here you can check out websites, etc and get some good ideas.