The question you should have asked, is not "Is a masters in computer engineering better than two years of experience at a company?"
Indeed, at that point in time, the two years of experience will put you in a better place than your masters.

What you should have asked was: "Is a masters in computer engineering + 2 years experience better than 4 years of experience?"
After masters + work experience will be more valuable, however, the masters cannot be a replacement for work experience.

Then again, I am doing my PhD in chemical engineering, so what do i know about a masters in computer engineering and your employability in the IT world...