I can give him my last name, get birth certificate as i am his father and get him canadian citizenship asap.
Don't do this. It will probably not work, since the visa officer may well become suspicious given the history of your relationship with your wife. If they ask for further proof or a DNA test, the application will be denied.
Will this cause problem for my wifes process? the CIC can object as How come i am married in 2009 and have a child born in 2002.
Yes, it certainly will cause problems. If you get the fake birth certificate, the visa officer will wonder about the history of your relationship with your wife. If the VO discovers the truth, your wife's PR application will be denied and she will be banned for two years from applying again for misrepresentation.
There is no reason to do things that way anyway. You can sponsor both your wife and her dependent child.