Based on the little information you supplied, I suggest you to go see a different accountant. My firm has branches all over the country and I only paid NY, NJ and federal taxes because I live in NJ and work in NY. Good luck.
You should only pay tax in your state and any federal tax that is due, if you are a member of a LLC. If you live in NJ and commute to NYC, there may be some commuter tax. LLC's usually issue a K-1 tax form . Keep a list of all your expenses and items you can depreciate(computers etc). You should keep your sheets (confirms & haircuts) for five years in case of an audit or tax related questions. I had listed some trader tax sites in another thread. I would suggest only using an account that is familiar
with trader tax's or has experience with traders who are
issued K-1's. Ask your fellow traders for a tax professional in your area.