According to New York's brochure for new drivers there are parts of New York in which you can drive alone when you have a junior license (not a junior permit) while there are still some areas of the state in which you cannot yet drive alone.
With a limited junior license you may not drive alone in New York City (the 5 boroughs) or in Long Island (Nassau and Suffolk counties) and Westchester, Rockland and Putnam.
With a full junior license you are not allowed to drive at all alone in the 5 boroughs that make up New York City. In Long Island (Nassau & Suffolk) during the hours of 5 AM and 9 PM you may drive alone only directly between your home and employment, a work-study program, a course at a college, university, or registered evening high school, a driver education course, or while engaged in farm employment.
The driver's manual as you noted states the following:
With a junior permit you are allowed to drive 5 AM to 9 PM in New York City (5 boroughs) but with these restrictions. You must drive only under the immediate supervision of your parent, guardian, person "in loco parentis," driver education Teacher or driving school instructor.
The person above must be at least age 21 and have a license valid for the vehicle being driven. Vehicle must have dual controls (dual brakes).
With a limited junior license the restrictions in NYC are:
No Driving Alone. You may drive under the immediate supervision of your parent, guardian, person "in loco parentis," driver education teacher or driving school instructor who is at least age 21 and has a license valid for the vehicle being driven. Vehicle must have dual controls (dual brakes).
With a full junior license it states you must not drive alone from 5 AM to 9 PM and that from 9 PM to 5 AM you must not drive in NYC. You should check with the NYS DMV to see if this means you can drive in New York City during 5 AM to 9 PM if you abide by the restrictions of a supervising adult that junior permit and limited junior licensed drivers follow.
The New York State Vehicle and Traffic Law though states that a junior license (class DJ) can not be used to drive in New York City at all.
The relevant section of the VAT is 501 paragraph 3c. Here it gives restrictions on use of class DJ and class MJ licenses. A class DJ or class MJ license shall permit the holder to operate a vehicle in accordance with the following restrictions:
"(c) in the city of New York, driving shall be prohibited."
The NYS Department of Motor Vehicles can give you more specific information on where you can drive with your junior license. Since the manual is not clear on if you can drive in NYC will a junior license we contacted the NYS DMV.
The representative that we contacted stated that a person with a full junior driver's license is not allowed to drive in New York City ( 5 boroughs). You will need to contact the DMV directly if you have more questions about restrictions on your junior license.