So if the President is aware, as you are, that his son should have been prosecuted, then why is he laying it on the DOJ?

Could be lots of reasons. He clearly loves his son, and probably just can't believe he's a bad enough guy to deserve a few years in jail, so DoJ must be wrong. He probably also believes (correctly) that this prosecution wouldn't have happened if Trump and the GOP hadn't attacked Hunter for so many years, and thinks that's something that's unfair of DoJ. He might also just be trying to preserve his legacy, thinking he'll be judged less by history if he argues that he's trying to correct an institutional wrong, rather than using a Presidential prerogative to help out a family member.

Regardless, if he's accusing DoJ of being unable to resist bending to the will of James Comer et. al., he's being grossly unfair to the agency - and weakening it at a time when it can ill-afford to be weakened.