I did not do a thesis during my MS program. The other two supervisors from my job post- MS can speak to research abilities, one in particular I worked with for quite some time on his projects.
That's what makes my third a tricky choice. One individual I did work with on 2 research projects, but again, was a fellow in my department at the time, but I kept in contact with them. Or, most recently, I did take two practicums with a professor from my graduate business program who can speak to purely academic and client interactions versus a professor I once took 7 years ago that I haven't kept in touch with. I really need strong letter writers, since personal circumstance affected my undergraduate GPA to only a 3.5.