Yes, the Town can Fine if Voilated the owner for Illegal apartments. The Town requires "Legal Accessory Apartment" Permit (if the owner lives in the house) and Whole House Permit.
I have the detail Rental Permit Application information, if you like I can fax it to you, please call me 631-889-2997 or email me @ firstname.lastname@example.org, your fax#...Good Luck..
Suggest that you contact their (Town of Brookhaven) accessory apartment department and have them send you a booklet on the fees, rules and regulations regarding the rental and maintenance of home based apartments. Generally rules in this area are extremely strict and very expensive if violated. Code enfoercement people take their jobs seriously with annual (or so) inspections, also neighbors can get upset about illegal rentals.