A store will be faster, but will involve waiting in lines. 9/21 will likely be the worst, but if previous years are any indication, the first 2-3 weeks will still see relatively long waits for the iPhone in stores. See if Apple does a reservation system like last year. They didn't on launch day 2011 and they haven't planned one for 2012, but depending on how crazy things get (or not), they might put one into place.
Of course, we can always hope that Apple has flooded the stores with iPhones the same way they did with iPads in March. Pre-orders sold out quickly, but stores were loaded with stock and so lots of people bought them in store and then cancelled their delayed pre-orders.