I'm a sole-proprietor independent contractor (sch c) and pay my mortgage for my home in Florida. My business is in NYC and I pay rent for the apartment. Ive been trying to sell the business but the economic situation has prevented it.
In the past, I have just been filing taxes in NYC and paying all three taxes but I'm wondering if I'm not losing a ton of deductions by being able to deduct the cost of rent.
One accountant tells me it's perfectly legal and another one tells me that I cannot do it. Any help?. Thanks.

The "perfectly-legal" accountant is probably referring to claiming the rent as a deduction as part of the Business Use of the Home option that is available to those who run their business out of their home.

You CAN do this, but only on a pro-rated basis for portions of the apartment that is used EXCLUSIVELY for the business, i.e. a completely separate room or office. The parts of the apartment where you live and sleep CANNOT be deducted.

I'm not 100% sure of this, but if the business owned the apartment or was the leasee, then it might be available as a deduction.