I would buy from online because then you are covered by Apple's rules regarding, say, returns within the 14-day period and, I suspect, repairs.
If, on the other hand, you buy from a store, you are at the mercy of their own rules. For instance, I bought a 4G iPod from an Apple store exactly 13 days before the 5G model came out. I tried to return it for exchange to the store according to the 14-day return Apple policy but the store had their own policy, so they would not take it back.
The short of it is, that if you are 100% sure and happy about your store, if you dealt with them before, then go with them. Otherwise, I believe that you are more protected by buying online. But don't forget, this was my personal experience...Others' might be different.
Ant