Middle English quene "a woman; a low-born woman," from Old English cwene "woman," also "female serf, hussy, prostitute" (as in portcwene "public woman"), from Proto-Germanic *kwenon (source also of Old Saxon quan, Old High German quena, Old Norse kona, Gothic qino "wife, woman," Middle Dutch quene "vain or worthless woman"), from PIE root *gwen- "woman." Compare queen (n.). The -ea- spelling is attested from early 15c.
Woman considered without regard to qualities or position (perhaps by contrast to the senses in queen), hence often a slighting or abusive term for a woman; in Middle English it could mean "a harlot; an old woman or crone," and it was in popular use 16c.-17c. in the sense of "hussy." But in Scottish often with a sense of "young, robust woman" (late 15c.).
The sense of "effeminate homosexual" is recorded by 1935, according to Partridge this was especially in Australian slang.