AN ACR LTT CLAIMS THAT GND CTLR CLRED HIM TO CROSS RWY 4L AND CONTACT THE TWR ON THE OTHER SIDE OF THE RWY. THE FO CHANGED TO THE LCL CTLR'S FREQ AS THE CAPT CROSSED THE HOLD LINE AND HEARD A BE02 BEING CLRED FOR TKOF ON RWY 4L. THE FO TOLD CAPT TO STOP AND THEY WATCHED THE BE02 TKOF IN CLOSE PROX. PHONE CALL TO TWR LATER DID NOT SEEM TO SATISFY THE CAPT RPTR.

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WHILE HOLDING SHORT OF RWY 4L AT BOS WE WERE CLRED TO CROSS RWY 4L AND TAXI TO RWY 9 BY THE GND CTLR AND TO MONITOR THE TWR AFTER XING RWY 4L. I THOUGHT THIS WAS SOMEWHAT UNUSUAL SINCE THE LCL CTLR FOR RWY 4L USUALLY CLRS TFC TO CROSS RWY 4L. KNOWING THIS I SWITCHED FREQS EARLY AND THE CAPT TAXIED ACROSS THE RWY 4L HOLD SHORT LINE. AT THIS TIME I SAW A BE1900 TAXI ONTO TXWY 4L FROM TXWY W AND WAS CLRED BY THE TWR FOR TKOF. I TOLD THE CAPT TO STOP; WHICH HE DID WITH ABOUT 1/2 OF THE ACFT ACROSS THE HOLD SHORT LINE. WE NEVER CAME CLOSE TO THE ACFT; HOWEVER THE SIT COULD HAVE BEEN DISASTROUS. AFTER RETURNING TO JFK; THE CAPT SPOKE TO BOS TWR SUPVR WHO SEEMED INDIFFERENT TOWARDS THE SIT. SUPPLEMENTAL INFO FROM ACN 361261: MY FO HAD SWITCHED TO TWR FREQ AND WAS CLRING HIS SIDE WHEN WE HEARD ON TWR FREQ 'CLRED FOR TKOF RWY 4L.' MY FO YELLED 'STOP!' AS THE BEECH 1900 WAS BEGINNING HIS TKOF ROLL APCHING FROM OUR R APPROX 100 YARDS AWAY. ALTHOUGH WE HAD CROSSED OVER THE HOLD SHORT LINE WE HAD NOT YET ENTERED ONTO THE RWY BEFORE WE STOPPED. THE BEECH 1900 CONTINUED THEIR TKOF WITHOUT INCIDENT AS WE HELD SHORT IN DISBELIEF. I BELIEVE THERE MAY HAVE BEEN TRAINING IN PROGRESS IN THE TWR BECAUSE THERE WERE DIFFERENT VOICES ON THE SAME FREQ. I BELIEVE THIS SIT COULD BE AVOIDED IN THE FUTURE WITH BETTER GND/TWR COORD; INCREASED OBSERVATION OF TRAINEES; AND CONTINUED PLT AWARENESS.