Choosing between two letters of recommendation
I don't think it matters too much if the academic letter is about a old relationship, or whether the work letter is actually from your job and not from academia. What matters is that the academic you interacted with has an excellent opinion of you - and that seems to be the case, given the many years in between! - and hopefully that the academic stuff you have been working together is related to your master. Similarly, your employer will have lots to say about your work aethics and dedication, and hopefully his academic background and/or your current job should be somehow pertinent to your masters.