My opinion on the stores I have been to:
Fish Factory: Kind of a "mom and pop" store, possible to find some good deals or rare fish but generally overpriced. Great for advice or just a good fish conversation. Not too many plants.
Hidden Reef: Close to the Fish Factory and the more professional seeming of the two. Pretty overpriced but with a nice selection, not many plants though.
The pet shack: Pretty small with little selection and little staff, had some shell dwellers though which surprised me.
Q-mart pet store (do not know the name): Great for big pieces of DW and has some decent plants.
Pets plus Quakertown: Pretty nice store an close to q-Matt store. Decent selection and not horribly expensive. Not much plants if I remember correctly.
Pets plus langhorne: Nice store with great selection. A fair amount of plants and a good selection of fish. Equipment selection is great.
Pets plus Norristown (formerly captain Nemo's): Getting better than they were right after the redo. A lot of show/large specimens. Not very good equipment selection but decent fish and plant selection.
Aquarium Center (NJ): Decent selection of equipment an a great selection of plants. Could not find any method to their tank organization but not a bad selection of fish.
That fish place: Best pet store I have been to personally. I wish they had slightly more plants but I may have gone towards the end of their supply. Amazing selection of equipment. I am pretty sure they have every standard size tank you can buy. Some staff seem knowledgable and some seem like teenagers messing around, but it is not hard to tell which you want to talk to. Good selection of FW and SW fish. Definetly worth checking out.
Hoping to go to the store in Clifton soon...