You have the right to be treated according to the same rules as everyone else, but you have to know your rights first. There are various federal, state, and City laws that protect people with disabilities. In some cases, these laws may overlap, interrelate, or protect a person when another one does not. Because of the complexity of these laws, one should seek the advice of an attorney before making a complaint.
The following links will take you to Community Resources that deal with issues of Housing.
Fair Housing Act
Prohibiting Discriminatory Housing Practices
Housing Preservation and Development (HPD)
NYC Affordable Housing Resource Center
Additional Barrier Removal
New York City Rent Guidelines Board
Disability Rent Increase Exemption (DRIE)
DRIE FAQ (in pdf)