Combine the flours, wheat germ, baking soda and salt in a medium bowl. In a large bowl, beat the butter and sugars with a mixer at medium speed until light and fluffy, about 3 minutes. Beat in the eggs, one at a time, until well blended, then beat in the vanilla. At low speed, add the flour mixture in batches until just combined. Using a wooden spoon, stir in the chocolate chips.
Position the racks in the upper and lower thirds of the oven and preheat the oven to 350 degrees F. Line baking sheets with parchment paper or silicone mats.
Drop heaping tablespoons of the dough onto the lined baking sheets, leaving about 2 inches of space between them (you should fit about 12 cookies on each baking sheet).
Bake until the cookies are slightly golden around the edges, 14 to 15 minutes. Let cool for about 3 minutes, then transfer the cookies with a spatula to a wire rack to cool completely (or for as long as you can wait).
To make sure the cookies bake evenly, switch the position of the baking sheets (meaning move the cookies on the upper rack to the lower rack and vice versa) and rotate the sheets from front to back halfway through the baking time.