There's a few factors.
Portugal are a more cohesive team than Argentina. ARG have had 5 managers since Portugal hired theirs.
Portugal's team is better overall than Argentina's. Argentina have better attackers but in every other area of the pitch Portugal trump them.
Rui Patricio > Armani
Semedo, Pepe, Dias, Cancelo > Foyth, Pezzella, Otamendi, Tagliafico
Moutinho, Carvalho, Neves, Bernardo Silva, Guedes, Rafa, Bruno Fernandes > Paredes, De Paul, Guido Pizarro, Acuna, Lo Celso and whatever other sorry bunch they called up this time
Portugal's opposition are generally easier. Their last World Cup qualifying group contained Andorra, Latvia and the Faroe Islands. The one before that had Luxembourg, Israel and Azerbaijan. UEFA's member nations dwarfs CONMEBOL's where Argentina are always having to play good sides like Brazil, Chile, Colombia and Uruguay.
Once they actually get to the World Cup and it's a lottery as to who they play I wouldn't say Ronaldo has performed any better than Messi has. Messi led Argentina to the final in 2014 while Portugal couldn't even get out of a group containing USA and Ghana. Ronaldo had one good game at Euro 2016 and they still won the thing even without him in the final. Without Messi Argentina would be even worse than they are with him which is bloody awful.