A female cat is called a Molly. She is only a Queen if pregnant or nursing. The term "queen" is sometimes used, but very seldom.
Normally "tom" or "tomcat" is used for the male, but there seems to be no commonly used corresponding word for the female.A male cat is called a tom cat which was named after a character in the book 'The Life and Adventures of a Cat' which featured a cat called Tom. It is also thought to have been named after the cat in the cartoon series Tom and Jerry although this is not entirely true.