You probably aren't likely to get a sourced, comprehensive answer for this, at least not one up to the standards of this subreddit (hope I can be proved wrong). It isn't necessarily a historical question. But the history of space travel can shed some light on the question.

Bottom line, two factors are at play here: space has historically been analogized to the ocean, and practical space travel in America came almost directly from the aircraft industry. Plus, the first and one of the hardest parts of spaceflight is ascent through the atmosphere, which has more in common with air travel (flight) than with water travel.

Different terminology is also used in different contexts. If you read documents from the space industry, you're more likely to see the term "spacecraft." The term "spaceship" is more likely to appear in science fiction, as it often plays on the analogy with oceanic exploration.

The American Aviation Experience: A History by Tim Brady gives you a simple textbook-style introduction to the history of the aircraft industry and its contribution to the burgeoning space industry in the 50s and 60s. Nearly every American aircraft manufacturer that played a large role in WWII contributed to the first American spacecraft. Boeing and Lockheed (and their joint venture, ULA) are still the primary manufacturers of spacecraft for the United States.

You can find the space/ocean analogy littered throughout fiction. Science fiction writers in the "Golden Age" especially were apt to use nautical terminology and themes to make their fictional systems more believable, and to further emphasize the analogy between ocean and space travel (see: Heinlein, Asimov, Clarke). Star Trek and Battlestar Galactica are just two popular examples in a long tradition of making spacefarers basically a navy. The analogy exists for a reason. Early transoceanic travel and space travel have a lot in common. They are both long-term, high-risk missions that require significant investment and brave participants. The vastness and emptiness of space provokes similar feelings to those that early explorers must have felt when looking out toward the horizon and seeing nothing but open ocean in all directions.