In ST-VOY S05E14 (Bliss), the alien Qatai refers to his ship in a non-gendered but anthropomorphic manner; even talking to it and giving it a command.
QATAI: Ah! Surprised? What's wrong? Can't figure out why I'm still not running, ha? Can't read my thoughts? Go ahead, attack, take my ship. Damn ship. Hold together. Hold!
QATAI [OC]: Don't bother. I know my ship. It's just being stubborn.
While not assigning gender, Qatai treats his ship like a willful co-pilot as much as an inanimate object. He has assigned it a obstinate personality and even barks orders to it.
Despite the hallucinogenic circumstances that he and most of the Voyager crew are under, his delusions do not extend to actually believing that his ship is a living entity capable of following his orders or manifesting a personality. Instead, he seems akin to O'Brien's penchant for anthropomorphizing the computers and machinery he works with.
Quotes courtesy of Chakoteya.net.