Will 2 years of non relevant work ex affect ms in cs prospects?
Every university is different, but two years shouldn't be a big problem as long as you haven't lost the knowledge you once had. But in the US, even that is less of a problem as the MS usually involves a lot of course work. 

Most admissions systems are looking for evidence of success that you can demonstrate. If your record is good and you can get good letters of recommendation you will have a chance. And, the internships and papers are a plus, of course. 

But note that, depending on where you apply, you may find tremendous competition for limited slots. Don't make your search for a university too narrow.