Combine flour, baking soda and salt in a large bowl. Beat together the butter, peanut butter, granulated sugar and brown sugar in a large bowl until light and fluffy, about 3 minutes. Beat in the eggs and vanilla until blended. Stir in flour mixture until well blended and dough forms. Stir in the chocolate chunks and chopped pecans.
Using a 1/4 cup measure, drop dough by slightly rounded mounds onto large un-greased baking sheet, spacing the cookies about 2 inches apart.
Bake at 325 degrees 15 to 17 minutes, until golden brown around the edges and lightly colored on top.
Remove from baking sheets to a wire rack to cool for about 3 minutes. Remove the cookies with a metal spatula from the baking sheet to a wire rack to cool completely.