Go to a bike store and see if they have some extra wheel boxes laying around. Ideally you can find 1x 2 wheel box and 2x 1 wheel box to see which is cheapest to ship. I have had it cheaper both ways. Make sure you get the little saucer things that go in the hubs. Rubber band your skewers up and put in ziplock bag and then duct tape it to inside of box. Fedex or UPS is likely to be about the same to ship in my experience.

Get a wheel box.

When I built wheels I shipped them in 26x26x6" boxes. One wheel to a box, wrapped in heavy bubble wrap. Then I taped the boxes together (cheaper shipping).