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Vital Throw hits first, then the other Pokemon Counters.
It's kind of like Focus Punch. Focus Puncher tightens its focus, Focus Puncher uses Focus Punch, Counterer uses Counter. Simple as that. Counter will always have last-priority in regard to move order.
As you can see, the assumption that Vital Throw always goes second is false. Counter has the highest priority when it comes to attacking last. Thus, it will go second even against attacks like Focus Punch, Vital Throw, etc.
@19jake93: No, Extremespeed doesn't have higher priority over Quick Attack; they both have the same. The faster Pokemon goes first in the event that they are both used. I.e. if a Arcanine used Extremespeed on the same turn that a Sceptile used Quick Attack, Sceptile would go first since his Speed is greater than Arcanine's.