The format what a [positively/negatively-qualified] noun is/are + [pronoun] is hopelessly archaic. Native speakers are familiar with it from an early age, because it survives in nursery rhymes...
Little Jack Horner ... said "What a good boy am I!"
The same non-standard "verb + subject" order is also "mocked" by Yoda's grammar in Star Wars...
Strong is Vader ... Strong am I with the Force
In modern English they'd always be expressed as What a good boy I am!, Vader is strong, I am strong.
It's also worth noting that "Isn't it a good song?" would never be expanded to "Is not it a good song?". This particular contracted format (and the "tag question" version "It's a good song, isn't it?") are very common today, but if a native speaker had to avoid contractions, they'd switch the order to is it not?
The "verb + [pro]noun" reversal of "It's a good song, isn't it?" is standard for tag questions (or indeed, any question of the general form "Is it a good song?"), but it's no longer current in many other contexts.
I see OP's second alternative "Isn't it a good song?" as a reordering of "It's a good song, isn't it?". It's not likely to be a genuine question - almost certainly the speaker thinks it is a good song, and doesn't expect an answer in the negative.
Because of potential conflation with the rhetorical/tag question form, if the speaker really didn't know, and was asking whether the song was in fact "not good", he'd probably say "Is it not a good song?"