It is hard for the unexperienced to discern what is a good store and what not. It is likely to be a small privately owned store over a large chain store, though neither guarantees anything. You could check if they have central filtration for all the tanks... (most have). That is not a good sign. All diseases will spread throughout the system. Selling pacu's, iridescent sharks and all of those monster fish to unsuspecting customers is a bad sign, just as selling goldfish for small tanks and bowls. Colored water from medications is a bad sign (unless it's not central filtration).
At some point you become experienced enough to see the quality/health of the fish though this isn't a guarantee as well as most diseases aren't visible with the naked eye. I have been doing it for over 40 years I look at the whole school/stock but LFS's are not the only problem there has been massive inbreeding at the fish farms the past decades, as long as the fish still lives at the LFS but dies after a couple of weeks at the customer, that's good enough for them, they go for that as long as you keep buying fish.
I have no recommendations for stores or sites, I personally no longer order online it is hit or miss. Done it a couple of times they can't even get the fish right. It is hard for me as well to get extra stock.
The best method would be to buy from hobby breeders, put an add on Craigslist for some fish, some people in your area might want to get rid of their fish. Maybe join an aquarium club.
