GCD is indeed lower-level than NSOperationQueue, its major advantage is that its implementation is very light-weight and focused on lock-free algorithms and performance.
NSOperationQueue does provide facilities that are not available in GCD, but they come at non-trivial cost, the implementation of NSOperationQueue is complex and heavy-weight, involves a lot of locking, and uses GCD internally only in a very minimal fashion.
If you need the facilities provided by NSOperationQueue by all means use it, but if GCD is sufficient for your needs, I would recommend using it directly for better performance, significantly lower CPU and power cost and more flexibility.