My two pesos,
Ship it via the airlines, tickets are still cheap and good to know that woofie made it when he gets dropped off in baggage claim at destination.
That being said, I used to ship dogs before flying (yes I was a pimp, but not a puppy farm pimp) and dogs don't do all that great in the belly of the plane. If it can fit under the seat, pay the money rather than put woofie in a dark cold compartment that scares the living dog mess out of them.
FF