Apple Store > Best Buy
There are many reasons I'd recommend buying an Apple product from an Apple store.
The staff at Apple are more knowledgeable. You wouldn't believe some of the things I've heard Best Buy employees say. There are also no commissioned sales people at Apple stores, which means that they are not going to pressure you into buying an overpriced extended warranty. Best Buy employees will say just about anything to get you to buy their extended warranty. I am speaking from direct experience. Apple Care will take much better care of you and costs less, and includes non-outsourced over-the-phone tech support at no charge.
As already mentioned above, when you make your purchase at an Apple store, they will open it up with you, activate it, register it, set up your mail, Apple ID, show you how to download, etc. all before leaving the store. Best Buy charges between $59-$119 for this same service through Geek Squad.
Apple stores have a wider selection of OEM iPad accessories, free workshops, and no restocking fees.