This is way too complicated. A couple of years ago I pedaled along the Delaware to Trenton, and ran out of daylight. Went to the bus station of a little New Jersey town, waited for a bus with my ticket, and asked the driver if it was okay if I slid my bike into the luggage compartment, fully assembled, panniers off and set to the side. Driver grunted, and it was done. We arrived at the Port Authority an hour or two later, I attached the panniers to the bike and off I went into the din and chaos of midtown Manhattan. But if boxing and reassembling is something you think you must truly do, please understand that the Port Authority Bus Terminal is a dysfunctional anarchy, and assembling a bike in some little trafficked corner should not be a problem, especially compared to the droves of homeless, the drunken brawls, and the occasional heart attack that is much more common. Just don't ask for permission, because whoever you ask will have to figure out how to clear it with their boss, who that boss might be, and what that boss might say...and it's just easier to say "no." Seize the day!