Include logo of cooperating company on thesis cover
The thesis is a scientific work, and it is the university that is responsible for it. The fact that you got someone funding you or that you performed the science somewhere else doesn't change this fact. I would keep the cover as simple as possible, and include only the university logo, and maybe even not that one.

Note that inclusion of logos of institutions that fund you seems to be a thing now. Sometimes rules are set up that the logo has to be on every slide of every talk that the people perform. This means that for some people, the slides are unusable, because they contain 5 or 6 logos. Some authors try to get their logo in an article they publish in the journal I typeset/copy edit; we have hard times explaining them that this is not acceptable in the journal and that only text acknowledgements are possible. Journals are quite strict on this, conferences commence to limit this as well.

Please, do not support this logo frenzy. If you really really want to include the logos, present them nicely in the acknowledgements section.