In a medium bowl, stir together flour, cocoa powder, and baking soda. Set aside.
In a large mixing bowl, beat together butter, the ½ cup granulated sugar, brown sugar and the ¼ cup peanut butter with an electric mixer until combined. Add egg, milk and vanilla; beat well. Beat in as much of the dry ingredients as you can with mixer (as the mixture will be very thick). Stir in remaining dry ingredients by hand. Form chocolate dough into 32 balls about 1 ¼ inches in diameter. Set aside.
In a medium mixing bowl, combine powdered sugar and remaining ½ cup peanut butter until smooth. Shape into 32 (¾-inch) balls.
Preheat oven to 350° F. Slightly flatten a chocolate dough ball with the palm of your hand, and top with a peanut butter ball. Shape the chocolate dough over the peanut butter filling, completely covering the filling. Roll dough into a ball. Repeat with the remaining chocolate dough and peanut butter filling.
Place dough balls 2-inches apart on ungreased cookie sheets or cookie sheets lined with Silpats. Flatten dough balls with the bottom of glass dipped in remaining 2 tablespoons granulated sugar.
Bake cookies in a 350° F oven for 8 minutes or until the cookies are just set and surface is slightly cracked. Let cookies stand for 1 minute. Transfer cookies to a wire rack to cool.
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