Preheat oven to 350 degrees F. Liberally grease 2 cookie sheets with non-stick baking spray.
In the bowl of an electric mixer, beat together margarine, sugars, egg and vanilla until smooth and creamy. Set aside.
In a large bowl, whisk together flours, baking soda and salt.
Combine margarine mixture with flour mixture and add chocolate chips; stir until well blended.
Drop 10 heaping tablespoons of cookie batter onto each prepared cookie sheet, about 1-inch apart.
Bake at 350 degrees for 12 minutes or until cookies are firm in the center.
Allow to cool on the cookie sheets before removing with a spatula and serving.
Tips
Whole wheat flour can go rancid very quickly. If possible, store in a sealable plastic bag in the freezer and only keep for about a month after openng. To test whether whole wheat flour has spoiled, sample a little on the tip of your finger. It should not taste sour.