It depends on what you want to do as an instructor and why you want to be one which you haven't disclosed yet.
depending on what you want out of being an instructor will depend on what you want to do.
pros of a shop: you can get a continuous stream of students, and it is likely a cheaper buy in because of rental gear, fills etc, and you may be able to get in on their insurance which saves you a lot of money
cons of a shop: you have basically no power, have to teach to however they want you to, aren't likely to make a lot of money, and that includes potentially having to buy gear that they get to dictate to you and teach in that gear
In big dive areas like cave country, very few instructors are officially teaching out of a shop. That said, they are "associated" with certain shops and they get things like free fills and gear discounts for bringing students into the shop which build a long term client base for them. In other areas, since most dive shops aren't run like actual businesses and they are penny wise and pound foolish, they don't think long term so it is very difficult to get deals like that as an independent instructor. They see them as threats to their business because they are pitched against other shops in the area or whatever other nonsense is going on. May be a NAUI shop against a PADI shop, or an Aqualung against a Scubapro shop, whatever it is, most shops perceive independent instructors as a thread and it may not bode well for you. As an independent instructor who doesn't teach that often, I don't really care what the dive shops in my area think, but I have access to compressors if I need them, own all of my own gear, and teach for very different reasons than most people.