Preheat oven to 350 degrees. In a bowl, whisk together flour and baking soda; set aside. In a large bowl, using an electric mixer, beat peanut butter, butter, and sugars until light and fluffy. Add eggs and vanilla, and beat until smooth. With mixer on low, gradually add flour mixture, beating just until combined. Stir in chocolate chunks.
Drop dough by heaping tablespoons, 1 inch apart, onto two large baking sheets. Bake until golden, 13 to 15 minutes, rotating sheets halfway through. Transfer cookies to wire racks to cool.