Don't think so. Naruto is full of Japanese Mythology and that stuff, and sometimes Kishi uses some Elements from other Animes and Mangas but I haven't seen any indication for mason-infiltration in Naruto. By the way how many symbols did they have. Most people can't tell the difference between the symbols of the Illuminati and those of the Masons.
Yeah that Eye of the Moon plan could be something but I don't think there is much behind. Every Supervillian want's to dominate the world. And in Naruto the strongest possible way is with eyes. And of course the goal would be to magnify your eye to get more people into it's ban like they did with the moon.
But aslong as they don't have people who use magic Eyes and Pyramids - apart from GARA

- I would say NO !