There are two parts to the fare you paid on Narita Express. This is an example on JR line. First, there is a base fare, josha-ken(乗車券), where Narita Airport-Shinjuku station is JYE 1450. If you take rapid commuter train, not Narita Express, from Narita Airport, then all you need to pay is JYE 1450.

On Narita Express you need additional express surcharge fare, tokkyu-ryoukin(特急料金), where on regular days the surcharge is JYE 1660. So riding Narita Express from Narita Airport to Shinjuku station on regular day will be total of JYE 3110. This is total fare on regular reserve seat, not Green Car. Green Car requires additional JYE 1290, total of JYE 4400 for Narita Express Green Car from Narita Airport to Shinjuku station on regular days.

However, there is high season and low season on express surcharge.

On year 2013 low season is Monday through Thursday of: January 16 – February 28, month of June, month of September, and November 1 – December 20.
During low season express surcharge is JYE 200 cheaper. Hence total of JYE 2910 on Narita Express regular reserved seat from Narita Airport to Shinjuku station. Again, Fridays, Saturdays, and Sundays are not considered as low season.

On year 2013 high season is all national holidays, March 21 – April 5, April 28 – May 6, July 21 – August 31, and December 25 – December 31.
During high season express surcharge is JYE 200 higher. Hence total of JYE 3310 on Narita Express regular reserved seat from Narita Airport to Shinjuku station.

In summary, Narita Express regular reserved seat from Narita Airport to Shinjuku station:
Low season JYE 2910
Regular days JYE 3110
High season JYE 3310