If we're allowed to count Jin's then maybe naruto/Bee.
If you mean natural then, 3rd raikage/Kisame by far have the largest.
You said, 'if you mean natural' then included Kisame, which stores and absorbs chakra in/with Samehada, i.e. not himself / not his own capacity.
Let's also remember than Nagato (through pain) said that Kisame had the most chakra out of all the Akatsuki, after Kisame had been hunting Bijuu (big oppotunity to absorb a LOT of chakra). This was also when Nagato was in his skeleton state, before that he would of almost certainly had more.
Third Raikage is sensible, and we don't have anything to compare him vs. Nagato, except that the Third Raikage battled the 8 tails until exhaustion of them both, which is an incredible feat. Where as for Nagato, in his skeleton state, through a series of weakened bodies destroyed an entire city, then destroyed sage mode Naruto (+help from others) and then, after all of this bought the Kyuubi to to it's knees with Chibaku Tensei; forcing it to become 8 tails to break out. We can't draw lines of Nagato used X amount, Raikage used Y amount, but we can say Pain's feat was also astonishing, especially considering his state.
Kisame was said to have the largest chakra out of all the akatsuki.
3rd raikage had the stamina to fight for 3days and 3nights, Like his son he most likely has bijuu level chakra.
Naruto and Bee both have more chakra than nagato also, They have their Own chakra plus the chakra of the 8/9tails.
Naruto and Bee do not have insane amounts of chakra, I believe somewhere we were told that Naruto's chakra is just a sap from the (for lack of a better word) leaking Kyuubi chakra.