Can my wife take my son out of state if we have already filed for divorce?

At most you should try to get a temporary hearing set up to discuss the custody of the child. The Court can order temporary custody until the final order is entered. What the Court cannot do is order your wife to return to the state. She has a right under the U.S. Constitution to travel freely and the Court can't infringe upon her right without having a compelling reason to do so. Her taking your son to live with her out of state is not going to be a compelling reason for the Court to infringe upon her Constitutional right to free travel and to live where she wants to. If the Court grants you temporary custody and gives her visitation rights, then at least she will have to return the child to you whenever her visitation rights ended, and you would have custody pending the findings the Court makes upon entry of the final order.