Realistically, SC. As far as in-game goes, Warcraft Units are argubkly stronger due to how the game engine works on WC, and they would most likely win. Seeing as most units in WC are like twice as strong as BC's and Carriers in SC, health wise and whatnot, WC Units would probably win.
But, if you guys remember, when they transported a few SC Units to the WC Engine, they were pretty powerful.