Cover letter for job application to someone I have personally met
I would lean toward the formal here, though it would be fine to remind the recipient of your past association, assuming it is professional and not personal. I doubt, however, that it is hugely important in most cases. But I also expect that you would already know if one or the other were greatly to be preferred. 

In follow up contact you might change that, depending on the response to your initial inquiry. If he replies back as John, then John it is. But your letter will be seen by several others, as noted by user Anyon in comments.