Petsmart does not sell rabbits. Not sure if petco does. However, occasionally those stores will host a rabbit rescue group and the rescue group will have rabbits available for adoption.
As a general rule, pet stores do NOT spay or neuter rabbits because it would increase the cost of the rabbits too much. Rabbit rescues routinely spay/neuter their rabbits because they don't want them breeding.
If you intend to get an intact rabbit and have a vet do the procedure later, then I'd highly suggest you call some local vets and ask their prices so you know what you're getting into. I have seen prices vary greatly. I have also seen a number of people on my rabbit forum complain that they couldn't find a vet near them to do the procedure for under $300.
Most rabbits will eventually need to be fixed for behavior. It helps them be more consistent with potty training, less destructive with chewing, and increases their chance for bonding if you decide, down the road, to get a bunny buddy.
Because surgery can be so pricey, it really is a bargain to get a rabbit from a rabbit rescue. Their rabbits are already fixed and cost less than the price of the surgery. Fixed rabbits are also more trainable and their personalities are evident (not so with babies). That means you can choose a rabbit based on personality.
You might want to check here for further info:
http://rabbitsindoors.weebly.com/choosing-your-first-bunny.html