This is a difficult question to answer since we don't really know the potential limits of either of them.

Bahamut is a primal and to some extent a 'god' but as the story progresses we are more and more questioning if the primals really are what they seem. We've seen that the regular elemental primals gain strength from worship so it would make sense to assume that Bahamut's strength would depend entirely on how much power he is receiving from worship. In this case Bahamut is receiving all of his 'worship' artificially from Dalamud so he's far stronger than the previous primals we've faced but if released from his prison I don't know how much power he would actually have since Dalamud itself appears to be the only thing keeping him summoned in the first place.

Nidhogg on the other hand is just a mortal dragon as far as we know. Having said that if you've finished the DRG storyline you'll have seen a demonstration of Nidhogg's power and he is very powerful. He is on a completely different scale to the so-called dragons we've encountered so far.

It's impossible to really say as we just don't know enough about either of them yet.