Line a 12-cup muffin pan with parchment squares so they come up over the sides, and set aside.
Whisk together the flours, wheat germ, baking soda and salt in a medium bowl. Beat the butter and sugars together with an electric mixer until light and fluffy, about 5 minutes. Add the eggs one at a time, beating well after each addition.
Mash the bananas with a fork in a separate bowl. Stir in the milk and vanilla. With the mixer on low, alternately add thirds of the flour mixture and halves of the banana mixture to the butter mixture, beginning and ending with the flour mixture. Mix until just combined. Fold in the chocolate chips.
Divide the batter among the muffin cups. Bake until a toothpick inserted in the center of a muffin comes out clean, 20 to 24 minutes.