Op,
He physically may not be brushing effectively even if he does it regularly. When he's laying on his back, you can do a secondary brushing even without toothpaste. Or when he's standing at the sink, stand behind him and do hand over hand.
Also, you may want to ensure that he's not eating too many acidic things or grinding his teeth. Lastly, cheese helps reduce the sugars that cause tooth decay:
https://www.ncbi.nlm.nih.gov/m/pubmed/1877906/
So ending a meal with a cheese stick could help.