I was wondering if I should get a letter of rec from my PI who I almost never communicate with or from the project manager (a grad student) who I work directly with.
I see your concern OP and am quite curious about how medical schools perceive a letter of recommendation from a graduate student compared to a professor? @Goro@LizzyM ?
Ask the PI. PI's will generally ask us who work with you for substantial input into the letter and/or for us to write it and he/she will just sign it at the end. Either way, always go through the PI.