I would agree with what OG says but add you have to compare the machines very carefully. Often the machine at Best Buy, or other big box store, is not the current machine you see at the Apple store. That is, Apple periodically "refreses" their machines with faster processors. The BB machine may not be that latest machine so the bargain price is actually for a previous iteration of the machine.
Best Buy in my area has a very bad reputation for taking returned merchandise and putting it back in stock and reselling it...so you get something bought, used a little, returned when you think it is brand new. Make sure the box has the Apple sealing and has not been opened and used.
The warranty is the same, whether Apple or a reseller. Apple honors that irrespective of the store it was bought from, unless it is a grey-market place then it gets dicey.