Just pump in some sleeping gas. Is it really necessary to call out ATF and DHS?
That may be the best chance to save the boy.
The pipe they use to lower the autism drugs and communicate to kidnapper Jimmy Lee Dykes is the key. With it they can put in a microphone that will pick up sleeping sounds. When it is obvious that Dykes is sleeping, they can send in a gas like Sevoflurane to put him in a deeper sleep. Then, they can breach the bunker and rescue the boy.