As long as the marriage was registered at a Thai Amphur and a certificate issued, the marriage is recognised and legal in the US. However, just a "Thai wedding" in the village is not.
Make sure your marriage certificate has been legalised in the US. It will be easier if your wife has an O visa as then she can be added to your Extension assuming your employer will do the paperwork.
First get the child their HK passport. The child can legally stay in Thailand but will need a passport to leave. Then you can get them an O visa to re-enter.