There is no way to accurately count the number of licensed charter boats in the state. You're not required to be a member of NACO or the charter association. However, you are required to be federally documented if you are running a charter boat and you must obtain a coastwise endorsement for your documentation. Additionally, any licensed skipper must also obtain a federal operator's ID card along with all federal permits required for the species being targeted which can range from mackerel to fluke and dogfish.
All documented and federally permitted vessels are available for view on the internet. I would guess one way of counting the official charter boats would be to look at an alphabetical list and count them.