Most all diets you see refer to uncooked. It really does not matter though, whichever you use, stay consistent, and your calorie decreases will follow accordingly.
Personally I find it easier to weigh cooked. Cook up a whole bunch and weigh them out. After a while, you will be agle to visualize your portion sizes even without a scale. I have been doing it so long, I can take a piece of meat and put it on the scale and be almost exact every time.