Definitely a reputable breeder, it takes hard work for breeders to earn their good reputation. When buying from a reputable breeder, you know for sure what the genetics of the geckos are. You likely will know whether the gecko is a male or female, or at least know what temperature they were incubated at. You'll also receive fairly good husbandry & care advice.
As for pet stores, there are some good pet stores that exercise proper husbandry and keep their geckos in good condition. But a good overwhelming majority of the chain pet stores do not follow that protocol. They place 5-10 geckos in a small display enclosure and keep them that way until they are sold. Many of them use sand, most of them dump crickets into the enclosures and leave them roaming for days. Oh and most don't supplement, which is why you see so many pencil tail geckos for sale in the stores. Many of which have MBD.
Breeders aren't perfect, and not all breeders are reputable breeders. But if comparing reputable breeders with reputable pet stores, I would pick the breeder over pet stores. Unless you are talking about one of those non-chain, specialized reptile pet stores that exercise good husbandry and care. Those pet stores I have no problems with.