You shouldn't just compare their arsenal. The feats that they've done is also a factor into this. They may have a weapon that's powerful than the others but if they don't know how to use it then it's just a pea shooter. I think the Chief would win. For he's fought way stronger than what the necromorphs could dish out. He's fought the Covenant, the Flood which is like the necromorphs in a sense. And even went head to head with the forerunners. Also Chiefs armor doesn't only protect him. The armor accelerates its users movement and reflexes by a lot. So much in fact that you need surgical augmentations to handle it. A normal human would die using the armor without the augments.
You also forget that Issac can use Stasis and yes the plasma cutter is powerful but it shoots PLASMA and what kills spartans in one hit? the energy sword which is made of PLASMA.So all Issac has to do is stasis him make the Plasma cutter go horissontal put it to his neck and bam he is dead.You also frget Issac can fly.
In a gunsblazing fight, that would be tricky. Chief has enhanced physical and mental capabilities and his Spartan armour while Isaac has the equivalent of Hermione's bag up his ass and a huge arsenal of gadgets and weapons. I would say Chief has the advantage, but the stuff Isaac's carrying is dead ass lethal to Spartan armour (assuming the shields are able to with stand such attacks).
And also, Isaac can only fly in zero gravity areas.