Depends to a great extent on what is being done, and whether or not the warranty is still in place. If the warranty is paying for something at the dealer, you wouldn't want to take it to Joe's Garage and pay for it. In the same way, routine things like oil changes would probably be cheaper at Joe's than the dealer, just keep a record of having it done. Once you're out of warranty, then Joe's for everything except things like reprogramming keys that ONLY the dealer can do.
As stated above, if under warranty the dealer but if not find an independent repair shop that has a good reputation and let them do the work for you.The dealer is paid off the commission of the extra parts that they will try and sell you and at the dealership you are known as a number no a person.An independent is paid off commission as well but a good shop will not stick you with unneeded parts.