Regulations surrounding the shipment of large lithium batteries has changed significantly in the past few years. Not only are passenger air carriers prohibiting large lithium-chemistry batteries, but domestic air freight companies are as well (UPS, FedEx, USPS). Customers seeking to ship large batteries by ground service might also run into red tape, as freight companies are increasingly requiring hazardous materials training.
At the present-time, traveling by air with your e-bike is fairly unfeasible, unless you have a spare battery on the other end of your trip. The motor alone tends not to add appreciably to the weight of the bike, so it can go in a bike box in the regular fashion. In addition, retail shipment of these batteries is also increasingly difficult (or expensive).
On the bright side, it is still easy to travel by domestic rail (Amtrak) with your e-bike and battery. You can even charge your batteries on the train if you are electric touring.