Want to get MS in Computer Science but in a predicament due to low GPA and lack of references I have a BS in computer engineering from a state school with a GPA of 2.56 (out of 4.0). I had a pretty serious and unmanaged illness from the second half of freshman year of undergrad to one year after undergrad graduation. I went from doing physical training for ROTC with no problem to throwing up from doing 7 jumping jacks. It practically happened overnight. When you look at my transcript, I have had probation over two semesters due to extremely low GPAs and a leave of absence due to illness. Yes, I could have taken a longer leave of absence while figuring out my health problem but I was told that I would lose my financial aid and would not get them back. I was advised to just plow it through since it would be the best course of action for me. 

A lot of courses I took had attendance integrated into the final grade. I would often get A's on exams but end up with C or B as the final grade. I tried explaining to professors that I was not physically able to get to the class to attend the lectures. Even with doctor's note (although it said "reason unknown/severe pain" at the time). Some professors even scoffed at me and told me to "take Tylenol and man up." 

I had the option of retaking some courses before graduation to improve my grade but that is when the state started cutting the budget so a lot of courses were canceled. I was stuck with F's in some instances without being able to remedy them. 

After graduation and finally being able to manage my health problem, I was able to refocus on education. Since I knew getting into a grad school with my academic record would be near impossible, I even considered going back to school for a second bachelor's degree in computer science. That proved to be a challenge since not many schools would accept me since my degree is too closely related to the major I am applying for. A lot of classes I should take to prove my competency for grad schools are not available to non-degree seeking students. If they are, those are only offered during work hours. 

Now I have 2 years of experience as a software test engineer (more like DevOps) and 1.5 years of experience as a software engineer. During my professional career, I learned a lot. And fast. I taught myself a lot of computer science topics since those courses weren't available for my major in undergrad (thank you 2008 financial crisis). I did not get along with managers at work due to differing opinions on how much/fast I should learn... Managers didn't like that I became de facto tech lead for some projects under a product as one of the most junior members in the company. 

Now that my background story is over... How do I approach grad school applications with my GPA? It seems near impossible to make up for the GPA while working. And how do I approach the letters of recommendation problem? I'm only able to secure one from a professor in undergrad days. My former colleagues at all levels are more than eager to write me letters. None of my direct managers nor other professors are willing to write me a letter. Managers from a different organization within the company are willing to write me one. Do those carry any weight? The ones not from direct managers/supervisors?
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.
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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.