As, I'm sure you know, a general rule is that you want to have two academic letters of recommendation. However, this general rule is often mitigated by many years of work experience and being far removed from the academic world.
There aren't any other professors you could ask for a letter? If not, and you don't want to tarnish your reputation, as you put it, just use the boss's letter.
Don't spend too much time thinking about this. Your letters aren't going to make you in any way. They are merely a formality. If you send them in, you're nothing special. If you fail to provide letters, that will hurt you.
In rare circumstances, a recommender will say bad things. That could hurt you. But more than likely, this won't be you.