Middle English ship, "seagoing vessel," especially a large one, from Old English scip "ship, boat, vessel of considerable size adapted to navigation," from Proto-Germanic *skipa- (source also of Old Norse, Old Saxon, Old Frisian, Gothic skip, Danish skib, Swedish skepp, Middle Dutch scip, Dutch schip, Old High German skif, German Schiff). Watkins calls this a "Germanic noun of obscure origin." OED says "the ultimate etymology is uncertain." Traditionally since Pokorny it is derived from PIE root *skei- "to cut, split," perhaps on the notion of a tree cut out or hollowed out, but the semantic connection is unclear. Boutkan gives it "No certain IE etymology."
Now a vessel of considerable size; the Old English word was used for small craft as well, and definitions changed over time; in 19c., a ship was distinguished from a boat in having a bowsprit and three masts, each with a lower, top, and topgallant mast.
French esquif, Italian schifo are Germanic loan-words. By 1590s as the name of a southern constellation (Argo Navis). When personified, ships usually were feminine at least from late 14c., but in 17c.-18c. masculine pronouns became more common, perhaps by influence of the use of man in names such as man-of-war, Dutchman, merchantman. In such combinations, man in the sense of "a ship" is attested from late 15c.
Phrase ships that pass in the night is from Longfellow's poem "Elizabeth" in "Tales of a Wayside Inn" (1863). Expression when (one's) ship comes in "when one's affairs become prosperous" is attested by 1851. The figurative use of nautical tight ship (the notion may be one in which ropes, etc., are tightly stowed) is attested by 1965; compare shipshape.
The model ship inside a bottle with a neck much narrower than the ship is attested by 1920. Ship of fools is in the title of the 1509 translation of Brant's Narrenschiff (1494).