My ex-girlfriend ran off with our son when he was 1. when he was 14 I found him and another man has been raising him since he was 3. She has a child support order on me established in 2011.DNA tests prove I am the bio dad. Can I appeal the order since he would be considered the father by estoppel?

No, you are the legal father, and as such will owe the support. If the paper work for the child support was not filed properly, if legal service not done correctly, you can challenge that.
The other man is has no legal standing and is like any step father, this does not apply to family law and child support.

If that man wants to adopt, then you may get out of support.

Lo l-do you KNOW WHAT exactly " Paternity by estoppel" mean?

If the order was established earlier you might get that to fly. Since it was only established last year, I'm less sure. Was the order entered after you re-established contact? Did you establish legal paternity/custody before she ran off? Was a visitation order ever established?
ANY question on law needs to include your general locale as laws vary by area.

As you can see, you didn't give enough info for us to give an accurate answer. I would suggest that you really need an attorney to deo this.