JFK levies the typical passenger service charge charged by many US airports (US$4.50 per movment) and it's the same regardless of the time between movements (arriving, departing.) If you fly into JFK and out of LGA, as co-terminals you still get the same charge.

Bottom line, airport taxes in the US are not especially onerous. It's fuel surcharges that you should be aware of.

Browse around this site for tax and surcharge information.