Destination charges are typically not negotiable. In fact, even customers who arrange to take delivery of a vehicle at the factory are expected to pay the full destination charge. You should obviously not be charged for it twice however. It is already included in both the MSRP and Factory Invoice (FWP) price.
The destination charge is the same for a particular vehicle no matter where the dealership is located (with the exception of Alaska and Hawaii in some instances). That's because manufacturers average the cost to ship a vehicle from the factory to the furthest dealership with the cost to ship a vehicle from the factory to the closest dealership. Some manufacturers do this for each model; others average costs across an entire make.
Destination charges are taxable, so the destination charge is added to the price of the vehicle before sales tax is calculated.