Very good question. He could have been interchangeably talking about both, but considering Ted mentioned the yin-to-his-yang, I definitely believe he was referring to Justin in that particular instance because he was at the time of this discussion the closest thing to Brian. Michael and Brian had definitely drifted apart by this time, though they were still friends... they weren't soul mates. However, I do believe Ted was talking about Michael, too, when he brought up the best friend part.