This is usually the worst place to shop for a bunny. Rabbits at a pet store are generally very cheap (under $30 usually), but call out to the impulse pet buyers. The staff is not usually well-informed about rabbits and are prone to making gender mistakes. The rabbits there are also usually from a bunny mill. They will be more shy and antisocial then a rabbit from another location. It usually takes much longer for these bunnies to warm up to you. Many rabbits from pet stores also die very quickly after going home with you, because they were separated from their mother at too young of an age, and are handling too many stressful changes too quickly.
There are many bunnies nationwide that are sentenced to spending the rest of their lives in a shelter, for no fault of their own. Rabbits aren't usually in shelters because they were bad; more often because the family situation changed. The family needed to move; a child went off to college; the family couldn't afford a bunny anymore; or they lost interest in the "Easter Bunny" (sad but true). Adopting a bunny from a shelter may not give you a purebred baby bunny, but it will give you a rabbit that needs a loving home, and usually one that is already "fixed" . Rabbits from shelters can possibly come with bad habits that it can take a lot of training to correct, but they can also come with good habits. If you want a house bunny, older rabbits are also easier to litter train usually. Many different rabbits of many different breeds, ages, temperaments and backgrounds can come from shelters.
Buying a bunny from a breeder is probably the most expensive, but it's the best way if you want a purebred baby bunny. Breeders get to know the rabbit's personality, what they like to eat and where they like to be pet. They place their pet baby rabbits in the best home suited for the bunny. They care about their rabbits first and foremost, and most breeders will take the bunny back if you cannot keep it anymore. They are knowledgeable about their breed and rabbits in general. Breeders allow babies to be weaned off mom slowly, at an age where they know the baby can handle the stress of being off mom's milk. Breeders only sell the babies at a time when they know the baby will be fine on its own, without mom or siblings.