Preheat the oven to 375 degrees F. Using a mixer on a medium setting, mix the peanut butter, margarine, sugar substitute and eggs until fluffy.
Add the flours, baking soda and extract and combine well. Using a wooden spoon, mix in the chocolate chips by hand. Refrigerate for at least 30 minutes.
Line a cookie sheet with baking paper. Using 2 moistened spoons, scoop up a heaping tablespoon of the mixture and slide it off with the other spoon onto the cookie sheet. Place cookies about 2 inches apart.
Bake for about 10 minutes, or until the bottom of the cookies are light brown. Remove from pan and cool on a grate. The cookies will harden as they cool.