I did a lot of research on this in June when I came home from school to finish up my PPL. I finally ended up training at AirFleet at Linden where I am now. I checked out pretty much all the schools at Farmingdale, ISLIP, Caldwell, Morristown and Linden. I can give you a run down of what I saw:
ISLIP. Pretty far out on the Island if you are coming from the city (especially with LIE traffic). There were two schools worth checking out there. Mid-Island had a large fleet and seeemed to be a well run place. They have another branch in Brookhaven which is about 20 miles east of ISLIP. Maintenance was good (I always check the ac logs when checking out a school). The planes were well kept. The prices for the planes were decent but there was something like a $250 training fee. FOR WHAT???? Fees like these are pointless in my eyes especially on top of already inflated NY prices. No thank you, I will look elsewhere!!!!
I also checked out American Flyers. This school has branches all over the place, even in Morristown if you live in Jersey. It is well run and very expensive. I did not get the chance to speak with any instructors or students as they will send a salesmen instead of a CFI to get you to sign up. The planes and the program seemed top notch though.
Farmingdale. I checked out almost all the schools on the field and there are many. I wasn't too impressed by any which was partly due to the ridiculously high cost of training on that field. Select seemed to be ok, they had all new planes and training was discouraged in the 152 since no instructors wanted to teach in it. Another JC user told me that they reallly shaft you moneywise by making you take extra flights that you don't need and charging bs fees and the like.
BK and Caleum seemed to be pretty run down. The CFI that gave me the tour of BK had absolutely no faith in the company although their Warriors did rent for $70 (which was the cheapest on the field). I had been warned by different people to avoid these places
Aviate Right is a joke. The guy running the place lied about everything, he claimed planes on the field belonged to the school when they clearly weren't. AVOID at all costs!!!
LIFT- I was impressed by this school's curriculum, maintenace and instructors, but the price was extremely steep (even for FRG).
Nassau Flyers- I heard good things about this school, they have a large fleet and have good maintenance, but there are so many fees here and there that it was clearly not worth it.
I may have checked out more, but this is all that comes to mind at FRG. I was not particularly impressed by any school so I took my quest across the river to Jersey.
Linden: Air Fleet was the only school on the field, it is small, uncontrolled and right below the Newark Class B. Air Fleet has a few instructors here, but its big base is at Teterboro. I chose to train here becauseat Teterboro you *WILL* spend a half hour on the ground waiting to take off and spend $6.50 on a landing fee. The planes seem to be in good shape (I checked out the maintenace at TEB and was impressed). I also found a more than decent instructor. The airport is on Rt1/9 a few miles off of the Goethals.
Caldwell (Essex Co.): Is not that far off of the GWB. They have a bunch of schools on the field.
Caldwell Flight- very good prices, but I heard some sketchy things about maintenace there. Was not too impressed by the facilities or the instructors.
Century Flight- run by a retired airline pilot/DE, this school is no BS. The planes are immaculate and the place is very organized. I took an intro flight with one of the instructors and was not too happy with him. I DEFINITELY would have gone here if I had not found a better instructor at Linden. Eagle went here for some training and recomended the place to me. I spoke to a few students there who spoke very highly of the place.
There is another FBO on the field (Air Dan or something like that). Nobody was there when I visited so I can not give an opinion. The prices seemed decent though.
Monmouth County is a little farther west of Caldwell. Thre were two schools there. American Flyers (see above) and Certified. Certified Flyers had fair prices and seemed to be a decent place.
I hope this helps, because it is a mess out there and I spent a lot of time researching all these schools. I would recommend Century at Morristown or Airfleet at Linden. Check out these places and see where you feel comfortable. But most importantly, prepareto pay. I did most of my training at OSU in Columbus and I pay about 1.5 times what I am used to for the same service. Remember to leave money for crossing the bridges too ( this is about $15 per trip plus gas for me).
If you have any other questions, feel free to PM me.
Good Luck !!!