Has she been driven in a car before? If so, what was her behavior?
If she has been fine riding in a car, then I strongly recommend this method of transportation. This way you always know how she is being handled and you can avoid any injury to her she could have flying in cargo.
There is a mild sedative a vet can prescribe before she would be put on the flight or to ride in the car. If she has a difficult time riding in a car, this sedative may be beneficial.
You would need to check with the vet to make certain the sedative can be given without causing developmental problems with the pups.
I hope this helps and good luck with mom and her pups to be!