N1 was the pioneer show. Definitely as a first launch it was brilliant and that's why I think that the first should not be compared with others.
Keeping N1 as a special case and away from my list, I would definitely go for N3 as the best season till date.
N3 was awesome. The characters were well etched and the motives against actions was clear. Bela was a deserving Naagrani, something that is rarely seen in the recent seasons. She was astute and had a command over her status. She wasn't loud or overly emotional while using her command, she was rather like a true leader; not accidentally chosen but born to rule. She was trained to be a queen and that's why her attitude differs a lot from Bani and Pratha. Mahir is the best ML till date. Not that the others were bad, Veer is a brilliant one too. But Mahir was a human and despite that he supported Bela in a manner never seen before. It was his humanity that made him heroic. Honestly speaking he was a true hero who went on to face supernatural enemies by the side of his Naagin Wife despite being a human. He paid the price for it too, but never stopped supporting Bela. BeHir were well suited and one of the best pairings till date.
N5 is the second best season for me. The storyline was not that good. It started well but they messed it up later. What was endearing to watch was the ML and his devotion for the FL. Veer had a single minded devotion for Bani. It was such a powerful premise - a love story between the leaders of two opposite enemy species. Yet Aakesh loved Naageswari from the first sight and his love transcended to the next life too. There was a lot more attention paid on the ML that made this series interesting because frankly I had too much of kitchen politics. Also the Cheel family was a male dominated family, the only female (who later turns out to be the villain) is kept locked for a long time. Bani was quite powerful and knew it. She did not have the training that Bela had of being a leader, but her brute force and aura of power often did the work. Also the chemistry was awesome. So of course the makers had to spoil it.
Beyond this, none of the other seasons come to my third preference. They are all a sore to bear (no offence - it's my personal opinion). I am not counting N1 as I have kept it beyond my list since it was the first one and thus has a separate place.
But N2 was a disaster that I barely remember. I saw two or three episodes and gave it up. N4 began well with the unique idea of the Naagin not knowing about her powers and exchanged children but went downhill and I was glad it got pulled off air. The show of Vampires started interestingly but I wish the leads were different. Frankly the actors didn't connect with me and the storyline dropped off. N6.... This one is a wretched season. Rishab is a ridiculous ML.. Even before the betrayal drama. Also characters and their motivations are very flimsy... They come and go. Too flimsy in execution and shallow exposition. Storyline is even more ridiculous. And loud... This season has too much in terms of depicting the storyline through dialogues rather than actions. Pratha is an undeserving Naagin and Mahek is a worse candidate. Rishab is not fit to be a ML and the crisis of the story keeps shifting as per the mood of the writers.
Well... I do hope they make good seasons again. Keeping fingers crossed for a good N7. They seem to have a good luck with odd numbers