The laws governing the legal use, storage and carrying of firearms are constantly changing. Below are the applicable laws in the State of New York as of 2/13/2013. The below information is designed to be a guide and not the final word. If you have specific questions, please refer to  the State of New York legislation at public.leginfo.state.ny.us.

It is illegal to carry any loaded firearm in any motor vehicle without a valid New York Permit/License to Carry.  If the person can legally own a firearm and the firearm is of legal obtainment you may transport a firearm through New York, if possesion of firearm is legal where the traveler starts and finishes; however Stopping in New York for an extended period of time with said firearms is in violation of New York state law.  While traveling without a permit/license through the State of New York firearms and ammunition must be kept in seperated lock boxes. Magazines and speed loaders must be empty and stored in a lock box as well. All items must be out of easy reach of all passengers.

NOTE: It is suggested that if you need to travel through the state of New York with firearms, you should carry a copy of Title 18-Part 1-Chapter 44 926A of the federal code.

Title 18 Section 926(a) The Peaceable Journey Act, under Part 1, Chapter 44, states:
”Notwithstanding any other provision of any law or any rule or regulation of a State or any political subdivision thereof, any person who is not otherwise prohibited by this chapter from transporting, shipping, or receiving a firearm shall be entitled to transport a firearm for any lawful purpose from any place where he may lawfully possess and carry such firearm to any other place where he may lawfully possess and carry such firearm if, during such transportation, the firearm is unloaded, and neither the firearm nor any ammunition being transported is readily accessible or is directly accessible from the passenger compartment of such transporting vehicle:

“Provided, that in the case of a vehicle without a compartment separate from the driver’s compartment the firearm or ammunition shall be contained in a locked container other than the glove compartment or console.”

You may find a copy of the Peaceable Journey Act/Title 18-Part 1-Chapter 44 926A here.