Honestly you need to do both! Kauai is so beautiful--and so much of it is only accessible by helicopter or boat--so you really do need to do both to get the full experience. The Napali Coast is gorgeous from the deck of a catamaran--you can see the towering sea cliffs from below while also being able hop off and snorkel in the sheltered bays and little caves. I like Makana Charters--the groups are small so the experience is intimate.
But then nothing compares to seeing Napali from the sky--so a helicopter tour is a must as well. You can see the Napali Coast, Waimea Canyon, and even Manawaiopuna Falls of Jurassic Park fame! I recommend Mauna Loa which flies out of Lihue. They have a doors off option and it's a private flight so you'll get a great seat. I hope the helps! Good luck!