"Boss" is a general word which means a person who's in charge of you at your work, s/he can also be the one who employs you.
"Employer" addresses a person, company, or organization that employs people.
"Owner" stands for a person or a group of people that hold the shares of a company so that they have the right to call the shots.
Having said that, the owner can be the boss or the chairman of the company. Nevertheless, sometimes s/he would rather recruit another individual for that position.
I hope this will meet your expectations