I have a one car limousine service which I have registered as a corporation car. I always have filed tax as self employed with income from my own business as well as getting
1099's in my name from other limousine services as a sub contractor. All expenses have been written off as expenses on my tax. I don't have any bank accounts in corp name or any 1099's in corp name.

I originally started corp to expand on my own but thought it was better to get work from established companies.

How do I clear up this mess? NY state is looking to see why I haven't filed the last 4 years.

You have to make the case with NY (and the IRS)that, though the business is registered as a corporation, you in fact ran it as a sole proprietorship.

Given the facts as presented, this should NOT be too hard to prove.

You need a local tax professional to help you in this matter. I recommend you contact an enrolled agent, who is a tax specialist licensed by the IRS. They tend to run cheaper than CPAs (though they are NOT cheap). Expect to pay at least $1,000 in fees. That said, I still would NOT present this case yourself if I were you. A negative decision by the state of NY could result in some heavy duty fines from NY, and you still have to straighten out the problem with the IRS.