What can I do to keep my wife from taking our son out-of-state?

If there is no court order in effect, than she can legally take your son out-of-state.  However, you can go to court and obtain an order which will require her to remain in the state (or return if she leaves beforehand).  If at that point she leaves anyway (or refuses to return) she can be charged with parental kidnapping.

The safest way for you to obtain legal custody of your son is for you to go to court first.  What you want to do is get a temporary order from the court on custody and visitation.  It will be temporary because a final decree will be issued upon divorce.  The court will consider the bests interests of the child in making its determination.  The court will look at the age of your child, the relationship of the parents and the child, the present living situation of the child, etc. 

Note:  If she leaves and establishes residency in another state before you file, then she can file for custody there. Again, you want to get before a judge before she does.

Right now, you need to consult with an attorney in your your area.