"My son does not go to school."
Translation:मेरा बेटा स्कूल नहीं जाता है।
I think that when negating a verb in Hindi, the word नहीं must go in front of the entire verb or verb phrase. So even if the verb consists of more than one word, as in the case of जाता है, the word नहीं must go in front of the whole phrase and become नहीं जाता है.
This contrasts the equivalent word "not" in English which goes in front of the main verb, but behind any auxiliary verbs in multi word verb phrases (i.e. "I do not go", "I will not go").
It's a matter of emphasis. If you say मेरा बेटा स्कूल जाता नहीं है , then a listener would expect you to follow up with where your son does go.
An attempt at equivalent English phrasing would be: "My son goes not to school, he goes home".
All that being said, I'm not entirely sure that मेरा बेटा स्कूल जाता नहीं है is strictly incorrect...?