How Good Is A Recommendation Letter For MS in CS From A Workplace If It's Coming From A Mentor?
Unless the MS is very applied, I'd think that an additional academic recommendation would be better. That is especially true if they can speak to different aspects of your work. 

But a letter from a mentor should, in general, be fine. It might even be better than one from a manager as the person likely has more knowledge of you and your contributions. The letter from a manager is likely to be a bit pro forma. The recommender should be clear about the relationship (i.e. mentor, not manager).