Letter of recommendation from employer
Yes, get the letter from your employer. In general, people reading letters want to see assessments of your skills, work ethic, etc., and these can certainly be provided by someone not in academia. Certainly if all aspects of content were equal, it would probably be more useful to get a letter from an academic, since it would likely map more directly onto likely success in Ph.D. research, but a strong and meaningful letter from your employer beats a weak and generic letter from a professor.