I think you ll have plenty of time if you travel by car service or have a vehicle available to you. If your thinking about using public transportation than i think you might be a little insane, lol.
Why are you staying in New Jersey if you want to go into Manhattan from La Guardia in Queens? You would have to start lining up hours before New Year s eve to get anywhere within a half mile of Times Sq. with a hundred thousand other people. You cannot do it because of a logistical problem that you described. You surely can make an attempt but you wont get close to Times Sq. until after midnight.
Don t fly into LGA, use Newark for a Jersey hotel. It s a shame there isn t anything cheap and safe to book in Newark since you could stow your stuff and then take the Path right into Herald Square and walk ten blocks uptown from there.If you wanted to use LGA, you should get a hotel in Queens near the airport or in Long Island City and then take the train in. Don t go to Secaucus from LGA. This would be madness.
Three hours is not long enough to get from LGA to Secaucus and then back to NYC by midnight. You might make it in time to watch the sanitation workers sweep the garbage left in the streets during the festivities.A better plan would be to go from the airport directly to whatever you want to do at midnight, and then check in at the hotel after midnight.
If your staying in Secaucus, you should fly into newark. If you want to go to Times Square, you re out of luck, most of those people you see on tv in the square have been there since before lunch.
You won t make it from the airport all the way to Secaucus in NJ and then back into the city by midnight. You should make reservations at a hotel in Long Island City (which is in Queens right across the river from Manhattan). That way you can check in, and then quickly get into the city probably by 11pm. Forget about Times Square, those people get there very early (like 10-11AM) and it is a ZOO.Overall the NYE experience in NYC is overrated. It just gets too crowded and hectic to have any fun. If you would like to go to a big club party or something along those lines I would recommend you buy a ticket from this site or a number of other sites:http://www.newyears.com/events/?zoneId=3��Try to get in town early to avoid lines, and good luck!