SpaceX May Be A Bargain For NASA, If Musk Delivers

"Boeing's cost structure is higher than SpaceX — that's just a fact," said Marco Caceres, senior space analyst at the Teal Group.

Because the aerospace giant has been around longer, it most likely has an older, more experienced workforce with higher wages and labor costs, he added.

But the biggest cost differences likely come from manufacturing processes. Boeing builds its Delta rocket and Atlas V launchers in a vertical position, while SpaceX's Falcon 9 rockets are assembled horizontally, which is easier and saves on time.

Meantime, SpaceX is a vertically integrated company, building all of its parts in-house, with no subcontractors. Boeing employs numerous subcontractors to build components, which adds to costs. "When you become a more established company, you can't be a specialist in everything," Caceres said.