They are often, but not always lower. This week the yellow labs at my local Petsmart were $8.95 if I remember correctly. Interestingly, from what I can tell, your LFS and the chains may often get their fish from the same sources.
I've had good and bad luck from both the chains and LFS. For example, neons from my then (I moved) local Petco were not good stock and I'd lose 4 out of five within the first week. No visible signs of diseases, just dropped dead even with drip acclimation. I had no problems and no losses with their glowlights and corys.
While I always look at general cleanliness, dead stock, signs of disease, I'm beginning to think that there is no way to absolutely assure getting healthy fish. There are ways to assure getting unhealthy fish, though. IMHO all we can do is increase the odds by getting to know each store, their general mode of operation, and the looks of their tanks.
If you see a fish you like at a good price and the fish, store and tanks look good, why not try it? Especially if you have a QT. I just set up my first QT after having a disaster with a batch of fish from a pristine and well regarded store. In the end I believe it was columnaris (cured by Maracyn 2) so it could have just been stress susceptibility and no ones fault really. I drip acclimated those fish, too. They started dropping within 48 hours. One of six survived. I spent more on meds than I did on the fish. Haven't been back to that store yet, but I don't really blame them either. I paid a premium for those fish, too.