I will try to give you a short answer, to make it less complicated. If you want to minmax, you have to take several factors into account. The main one is, where are you planning to hunt?
Lion rod I won't include, because for rather obvious reasons, it's not a great rod.
Naga rod: magic lvl 2, ice magic lvl 2, protection fire 4%:
Notable difference in proficiency: Ice oriented. 3% crit dmg from ice spells and runes and 2 ice magic lvls. The rest is not relevant
Falcon rod: magic lvl 3, energy protection 8%
Notable difference in proficiency: mana on kill/crit hit chance for terra wave, 5% of your ml as extra dmg for spells, earth ml+1 and 5% critical extra damage.
The answer of which one is best depends. Personally, most of the time when I hunt solo, I am using avalanches so I would just pick the Naga rod for these situations. If I would be stepping into a spot where I play with other people, where I can use waves, which I won't do on solo, Falcon rod is the superior choice.
But if I was level 300 and I could only select one, COBRA ROD is the best choice. It's a more all-round balanced weapon, decent wheel and the extra life leech bonus is very comfortable. It beats Falcon rod in TH spots too most of the time, and it will make your life easier.
So no, I wouldn't agree the Naga rod is underrated. It's decent for solo hunting, but not much else. It has some minor uses where mobs are strong/immune against earth, like cobra bastion. But besides this, it's not great.