What is the difference between M&P 40 model 206300 and model 209000
Of the two .40 models which one is better?

206300 has the thumb safety.
209000 has the mag disconnect and internal lock.
209300 is what I'd get. No thumb safety, no mag disconnect, no internal lock. But it's a matter of personal preference of course.

Are these model numbers located on the pistol?

No, they are the product code or SKU#. You can find most of the model features on the S&W website, although they will add or drop certain models at times.