The measure word for ships is 艘 (sōu). 军舰 covers all types of warships. More specific: 航空母舰 (hángkōng mǔjiàn, aircraft carrier), 驱逐舰 (qūzhú jiàn, destroyer).
usage
军舰 (warship) vs 船 (chuán, general boat/ship) vs 舰艇 (jiàntǐng, naval vessels, more formal/collective term).
