Not sure about NY but in Florida I use their pass and it counts axles based on the one pass in the truck. Cost with a tandem axle trailer is about 3 times the cost of a car or pickup.
Not sure about New York, but you are right - the Florida Turnpike systems have in-road sensors that count axles. Fortunately, they run on a simple axle-based system. Looking at the New York Thruway website, looks like they use the more complicated height- and axle-based systems typical of northeast corridor EZ-Pass authorities.
As someone that works as a software engineer in the toll industry, I always groan when we win a contract in the Northeast. Their complicated tolling calculations always cause us a lot of heartache. Fortunately, another company has a pretty good lock on the EZ-Pass systems, so it's rare we have to get into that mess.
Also, a hint if you do have a SunPass (Florida) tag and use their roads - check your statements carefully when you are pulling your RV. Most of their roads still use an older method of counting axles that still occasionally counts a two-axle trailer as a three-axle trailer. First time I drove up the turnpike from Orlando, I checked later just out of curiosity and one of the tolling points counted my pickup and two-axle Big Country as a five-axle vehicle. They're pretty good about correcting issues if you contact them.
For trivia sake, here's an installation of the software I work on being tested by a Corvette traveling at 200 mph. Not shown in the video is the fact that we successfully read the Texas toll tag mounted on the car's windshield. Also, the car traveled down the center of both travel lanes which is a move many people think is cheating the toll system. Fact of the matter is that we use four cameras per lane (two front and two rear) to take pictures of the vehicles passing through. Drive down the center of the two lanes and we get a total of 12 images of your vehicle (4 front and 8 rear), most of which will have a legible license plate. Just thought you'd like to know.
http://youtu.be/B-gzNi6MRwI
