Hmmm - the other writeups here are being nuked. So I'll add in the info from those (from no bye no aloha and Powers).

The New York State Thruway system, officially named for Governor Thomas E Dewey, is a 641-mile long network of freeways in New York state, maintained by the New York State Thruway Authority (NYSTA). The first section, from Lowell to Rochester, opened June 24, 1954. The whole tolled Thruway system was open by December 23, 1960. Since it is tolled, there are many service plazas with food and gas along the way.

There are four sections of road on which the NYSTA collects tolls:

The NYST mainline stretches 496 miles from the Major Deegan Expressway (Interstate 87) at the New York City border to Interstate 90 at the Pennsylvania state line near Erie. It passes by the metro areas of New York City, Newburgh, Albany, Utica, Syracuse, Rochester, and Buffalo, costing $17.70 (eastbound) and $14.70 (westbound) by car from end to end. It is in no way the shortest route between Erie, Pennsylvania and New York City; that is accomplished mostly via Interstate 86/State Route 17, the Southern Tier Expressway and Quickway. However, the Thruway avoids the mountains of the Southern Tier, running along the route of the Erie Canal and the New York Central Railroad's Water Level Route. The Thruway carries Interstate 87 south of and Interstate 90 west of exit 24. Interstate 287 is also on the Thruway from exit 8 to exit 15.

The Yonkers toll plaza, between exit 6A and exit 7, is the southernmost, charging 50 cents (for cars). Next is the Tappan Zee toll plaza, between exit 9 and exit 10, charging $3 southbound/eastbound only to cross the Tappan Zee Bridge. The Spring Valley toll plaza, between exit 14A and exit 14B, charges no toll for cars, and a northbound/westbound only toll for trucks. In the southern region of the Thruway, traffic not passing through one of these toll booths rides for free. The Woodbury toll plaza lies within exit 16. Northbound traffic receives a ticket and southbound traffic hands in their ticket and pays. Traffic to/from the south (exiting northbound and entering southbound at exit 16) pays 50 cents. Traffic entering northbound pays 50 cents at the same toll booth as traffic to/from the south, and then gets a ticket at a side area of the mainline toll booth, with prices about 50 cents less than traffic coming from the south. Traffic exiting southbound exits before the mainline toll and hands in the ticket at the plaza at which other traffic pays 50 cents. From there all the way to the Williamsville barrier, between exit 49 and exit 50, the Thruway uses a ticket system, in which entering traffic gets a ticket listing prices to exits, and exiting traffic hands in the ticket and pays. Westbound traffic pays and eastbound traffic gets a ticket at Williamsville. The Thruway is free until the Lackawanna barrier, between exit 55 and exit 56, where the ticket system starts up again until the Ripley barrier, between exit 60 and exit 61. Westbound traffic gets a ticket at Lackawanna and pays at Ripley; eastbound traffic gets a ticket at Ripley and pays at Lackawanna.

The Berkshire Extension connects exit 21A to the Mass Pike (Interstate 90). East of exit B1, it carries Interstate 90; west of exit B1 it is unsigned reference route 912M. Tolls use a ticket system connected to the mainline system; traffic entering at the Massachusetts state line can go to Buffalo on a single ticket. The Canaan barrier toll lies between exit B2 and exit B3; traffic between exit B3 and the state line doesn't pay in New York but must go through the toll booth in Massachusetts. Though the Mass Pike is now free for cars west of exit 6, there are still toll booths for trucks and traffic going past exit 6.

The New England Section carries Interstate 95 from New York City to Connecticut. The southern end is at the Bronx and Pelham Parkway interchange (exit 8) and the northern end is at the Connecticut state line. The only toll is $1 northbound only at the New Rochelle barrier, between exit 16 and exit 17.

The Niagara Section carries Interstate 190 in Buffalo and Niagara Falls, from the Thruway mainline (Interstate 90) to Ontario, where it becomes the 405. However, the road is only maintained by the Thruway Authority south of exit N21. The southernmost toll booth is the Buffalo barrier, which charges 50 cents northbound only, and lies between the south end (at the mainline Thruway, which is free here) and exit N1. The Black Rock barrier, between exit N9 and exit N11, charges 50 cents southbound. The Niagara Section crosses over Grand Island between Buffalo and Niagara Falls. The Tonawanda barrier charges 50 cents northbound to enter the island from Buffalo, and the Niagara barrier charges 50 cents southbound to enter the island from Niagara Falls.

In addition, several free roads are maintained by the NYSTA.

The Garden State Parkway Connector connects the mainline Thruway exit 14A to the Garden State Parkway in New Jersey. It is totally free north of the School House Road interchange, but traffic staying on south of School House Road must pay a toll in New Jersey.

In 1991, Interstate 84 and Interstate 287 (Cross Westchester Expressway) were added to the Thruway system. They are not tolled but are maintained with toll money from tolled portions of the Thruway network. The Newburgh-Beacon Bridge is maintained by the New York State Bridge Authority (NYSBA) but Interstate 84 on both sides is maintained by the NYSTA. I do not know whether the short section of Interstate 287 between Thruway exit 15 and New Jersey is maintained by the NYSTA or the New York State Department of Transportation (NYSDOT).

Sources:
http://www.thruway.state.ny.us/faq/index.html
http://www.thruway.state.ny.us/tolls/calc/trip.cgi

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