I'm sure they will honor the online price if you ask the downtown store to do it, but for other items, the pricing reflects the MUCH higher cost of business across the locations. In fact it's common for national chains to exclude NYC locations from discounted promotions. You may think it's gouging, but it's a reflection of 1- high cost, 2 - high need for the customer to get it right now, instead of waiting.
In case you haven't learned yet, Time = Money