NY State does NOT permit the carriage of rifles while loaded.
In NY State, a magazine with cartridges loaded (no matter how many cartridges are in the mag) is deemed to have your rifle in a *loaded* state for purposes of transportation.
So, the question to the OP...why do you want to carry your rifle in your car with loaded mags? Simply lock up the rifle with its magazines in your rifle case, then lock up the ammo in the glovebox.
The only time you can transport the rifle (still must be locked in the trunk) and have a mag on your person with cartridges inserted is while hunting provided that:
1) the area you are hunting (these are known as NYS DEC Zones) does not specifically ban rifle hunting...
2) you are *actually* hunting...ie: you have your hunting license prominently displayed on your person (usually on the back of your jacket) while in possession of a loaded magazine and...
3) it actually *is* hunting season for the game you are claiming to be hunting.
As for having a CCW in NY and carrying a loaded rifle...you CAN'T do it. CCW is a HANDGUN ONLY license. Has nothing to do with the carriage of rifles/shotguns/long guns.
Do yourself a favor...if you're in NY State, read the laws. Just Google up NYS Penal Code 400 and NY Penal Code 265...but I'll do some of your homework for you to show you that jrmiddleton, while wanting to be helpful, is not quite correct.
From Penal Code 265.00 Definitions, #15...
15. "Loaded firearm" means any firearm loaded with ammunition or any firearm which is possessed by one who, at the same time, possesses a quantity of ammunition which may be used to discharge such firearm.
Possession, according to Penal Code 265, means being in control of the loaded mag. In other words, you're the driver of the vehicle, you have, under your control as the driver of t he vehicle a rifle which has a magazine, said magazine is loaded and in the glovebox while the rifle is in the trunk...you are now guilty of transporting a loaded firearm. Period. No ifs-and-buts.
NY State does NOT mess around, either. You get caught, you'll need a real good lawyer.
So...is a bit of *convenience* for you to load mags up so that you *don't have alot to carry around* worth the risk of getting caught, and having a future CCW application denied because you were once caught transporting a loaded weapon (loaded in the eyes of the law and in accordance with NY Penal Statutes...)