My 3 and 4 year old children have not seen a doctor. Sincethe youngest was 4 months old, I used to believe thatimmunization cause autism. Now I want to catch them up, but fear that the doctor will call this neglect. Both of them are healthy. What to do?

It is not neglect. An initial poor choice that you now understand and want to rectify is not neglect. Please proceed with the immunizations for your children. Without these the risk of major disease is significant.
Do the right thing. I am sad you were caught up in the misinformation spread about vaccines and autism.Unfortunately this hoax has led to dozens of preventable deaths every year when their parents avoided the vaccines. I encourage you to get in and get them caught up. I consider the vaccine skippers misguided, not neglectful, and most physicians will welcome you and praise you decision to catch up.
Take them. Simply explain to the doctor what happened. Many folks withheld vaccines due to the fake data from that guy. You are not alone.