Tough battle. Vision's immune to J'onn's telepathy and could detect him even if he went invisible, both can phase, both have eyebeams, both can fly, both have decent super-strength... In the end, I think Martian Manhunter's super-speed and shapeshifting would give him the win, though.
If we're talking about the Young Avengers' Vision, who has Kang's shapeshifting armor with greater firepower in place of his old body, it might be a different story. He'd probably be able to keep up with J'onn better, but I doubt he'd be able to beat him because of, again, the super-speed.