1. Preheat oven to 375 degrees. Line a 12-cup muffin pan with paper liners. In a bowl, whisk together flours, wheat germ, baking soda, and salt.
2. In a large bowl, beat butter and sugar with a mixer until light and fluffy. Add eggs, one at a time, beating well after each addition. In another bowl, mash bananas with a fork; stir in milk and vanilla.
3. With mixer on low, alternately add flour mixture and banana mixture to butter mixture, beginning and ending with flour mixture; mix just until combined. Fold in walnuts and chocolate chips.
4. Divide batter among muffin cups. Bake until a toothpick inserted in the center of a muffin comes out clean, 25 to 28 minutes, rotating pan halfway through. Let cool in pan 10 minutes; transfer muffins to a rack to cool 10 minutes more.