Whom should I ask for letters of recommendation?
Ideally, you do want letters of recommendation from academia.  That being said, graduate schools (especially for PhD programs) are all about research and not so much about coursework, so you would want a letter to describe how you have the potential to succeed in a research setting.  The industry connection may help you do that, but you haven't provided too much detail on how you worked under that person.
I mentioned this in a comment above, but have you done anything outside of research where you interacted with professors (including TA'ing a course)?  That is also a valid source of getting a recommendation letter.  In addition to this, who would you be thinking about for that third recommendation letter from what courses and why?  It's never too late to try and send a quick e-mail and/or have a conversation in their OH to try and see if you/them remember each other.  Maybe talk about how interesting their class was, what your plans are in the future, or maybe how interested you are in their field/research.  (As a recent graduate, I occasionally try to send a quick e-mail to get advice from professors, especially since with COVID things are largely virtual, and maybe see if I want to ask them for a recommendation down the road, since I am also in the same boat)
When would you be applying for graduate programs?  Maybe you could try to TA a class or get an additional research experience in before you do so, and by extension, that third recommendation letter that you need.