CHARTER FLT CONFUSED REF TAXI CLRNC.

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MY FIRST INDICATION THAT WE MIGHT HAVE CROSSED A RWY WITHOUT CLRNC WAS WHEN WE ADVISED TWR THAT WE WERE READY FOR TKOF AND THE TWR CTLR SEEMED SOMEWHAT SURPRISED THAT WE WERE ON THE E SIDE OF RWY 3 ON C TAXIWAY AND ASKED US WHICH RWY WE WERE USING FOR TKOF. WE THOUGHT (MAY HAVE ASSUMED) RWY 36. IN RETROSPECT WE WERE UNSURE WHICH RWY WE HAD BEEN CLRED TO ORIGINALLY; BUT HAD BEEN APPARENTLY CONFUSED (UNAWARE) BY SOME OF THE INSTRUCTION WE RECEIVED FROM GND CTL. WE RECEIVED TAXI INSTRUCTIONS TO DEPART THE RAMP AND FOLLOW THE LTT AHEAD OF US TO THE RWY. WHEN THE LTT WAS APCHING THE INTXN OF TAXIWAYS A AND C IT WAS DIRECTED TO FOLLOW THE ACR LGT ON TAXIWAY C TO RWY 36 AND ANOTHER ACR MLG HOLDING ON C TAXIWAY WAS DIRECTED TO FOLLOW THE LTT TO RWY 36 AND WE WERE TOLD TO GIVE WAY TO THE MLG AND FOLLOW IT TO RWY 36 OR WAS IT 3 (WE THOUGHT OR ASSUMED 36). IT WAS WHEN WE CALLED THE TWR READY FOR TKOF WHILE ON TAXIWAY C E OF RWY 3 WHEN WE GOT OUR FIRST INDICATION THAT WE MAY HAVE CROSSED RWY 3 WITHOUT CLRNC TO DO SO. I SUSPECT THAT THERE WAS NO CLOSE CALL AS WE CROSSED RWY 3 RIGHT BEHIND THE MLG AND WERE NOT ASKED BY THE TWR CTLR WHY HAD WE CROSSED RWY 3 WITHOUT CLRNC. HUMAN FACTORS: THERE WAS SOME SENSE OF URGENCY FOR THE CREW; AS WE WERE TRYING TO ARRIVE AT JFK PRIOR TO 1500 (L) AFTER WHICH ARO'S ARE REQUIRED AND WE DIDN'T HAVE ONE. THIS MAY HAVE CAUSED SOME DISTR FOR US. THE TAXI SEQUENCING AND INSTRUCTIONS TEND TO MAKE US THINK THAT WE WERE CLRED TO RWY 36 INSTEAD OF 3. ALSO AT THAT TIME NO OTHER ACFT IN FRONT OF US HAD BEEN CLR FOR A RWY 3 DEP AND SEEING ALL THE OTHER TURBOJET ACFT DEPARTING RWY 36 WE MAY HAVE WRONGLY ASSUMED THAT WE WERE DEPARTING FROM RWY 36 ALSO. I ALSO SUSPECT THAT THERE WAS SOME CONFUSION ON THE PART OF THE GND CTLRS FOR IF IN FACT THEY HAD INTENDED A RWY 3 DEP FOR US THEY SHOULD HAVE (AS LOGIC WOULD SEEM TO DICTATE) INSTRUCTED US TO TURN R ON TAXIWAY B FROM A (INSTEAD OF FOLLOWING THE MLG ON C TAXIWAY) IN ORDER UTILIZE THE FULL LENGTH OF RWY 3. ADDITIONALLY AS RWY 3 IS ONLY 4905 FT AND RWY 36 IS 6869 FT IT WOULD SEEM THAT IN MOST CASES RWY 36 IS THE PREFERRED RWY FOREMOST TURBOJETS. THIS FACT IN CONJUNCTION WITH OUR COMPANY POLICY OF NOT NORMALLY USING RWYS SHORTER THAN 5000 FT MAY HAVE INFLUENCED OUR PERCEPTION THAT WE HAD BEEN CLRED TO RWY 36 AND NOT RWY 3.