Man, I for one am pretty damn torn. It's very very hard to say how large Madara's Chakra reserves are; impossibility hard. He did last till the very end against Hashirama who went into Sage Mode as well, with the same Chakra reserves without any addition of Natural Energy. SM is technically a careful mingling of Nature and Self, hence it's not as easy to suggest anything here. Hashirama won just by a hair, really. It was an even fight.
Nagato is Uzumaki, and hence, should have naturally large chakra reserves, but that is not to say that Uzumakis have the largest Chakra reserves. The Raikages' and Kisame also have extremely large reserves. I am going to go with the third option.