Want to get MS in Computer Science but in a predicament due to low GPA and lack of references
I think your experience in industry will appeal to master's degree admission committees. Your application/cv should describe your technical skills. Get letters from your coworkers that speak to your competence with them and your ability to learn.
. 
Your cover letter can talk briefly about your health problems as an undergraduate. 

I don't know whether the absence of letters from your direct managers will matter. If I were interviewing you for a job it would matter to me, but for a master's degree I might well want to take a chance.