Top 5 Shinobi with the Highest Chakra Levels you say? Lesse....
1. Naruto (has the potential to. Most instances he isn't, but when he gains more power from Kurama, he does)
2. Hashirama (Edo Tensei just means he won't run out of the chakra he has, not "has more chakra than before death")
3. Madara (this is, of course, the next step down. We've seen what he can do, but on a comparison to Hashirama, he used external chakra sources (Kurama) to help him in his fight. There is no evidence indicating the Rinnegan boosts chakra levels, but the Senju DNA likely can. It's too bad Madara is in Edo Tensei mode to test this idea.)
4. Kisame (Kisame has a freight load of chakra. The problem is, he doesn't have the epic ninjutsu to push his chakra to the limit. He doesn't own any extreme-level ninjutsu, unlike the others on this list.)
5. Nagato (Nagato has less chakra than Kisame, but has the powerful ninjutsu to test the boundaries. This is where people get confused--they see Nagato being able to execute powerful ninjutsu and assume his chakra levels are much higher than Kisame's. While he does have a lot of chakra, he doesn't have nearly as much as the other four on this list. He was able to endure a lot of strain because he's an Uzumaki, the clan reputable for being a sonuva***** to kill).
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Higher chakra level does not necessarily mean the shinobi will win above all others. This is not what this top 5 list is trying to prove.