I suspect it was a shortening of watercraft. According to wiktionary the use of the word for water vessels was originally used for smaller loading craft. So using the older Germanic meaning of "by means of", the phrase "it got here by watercraft" could be translated as "it got here by means of water". One could assume that it wouldn't take much for the word to go from preposition to noun; especially in the context of agglutinates and abbreviations.

The English word "boat" comes directly from German; "das Boot".