A LARGE ACFT IS CLRED FOR TKOF AT THE SAME TIME TWO OTHER ACR ACFT ARE CLRED TO CROSS THE SAME RWY.

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EWR WAS BUSY; WE HAD A 30 MI FINAL AT 170 KNOTS. ON A 5 MI FINAL; TWR HAD AN ACFT LOSE SIGHT OF THE VISUAL TO RWY 29; TWR HAD TO GIVE MULTIPLE RADIO CALLS TO ASSIST THE ACFT WHO HAD SEVERAL OF THE CALLS REPEATED. THERE WERE ALSO NUMEROUS STEPPED ON RADIO CALLS ON TWR FREQ. AFTER LNDG ON RWY 4R WE WERE TOLD TO HOLD SHORT OF 4L ON KILO BEHIND ACR Y. WE WERE THEN CLRED TO CROSS RWY 4L WITH ACR Y AND HOLD SHORT OF TAXI S. ACR Y STARTED TO CROSS; BUT STOPPED. WE THEN SAW AN ACFT TAKING OFF ON RWY 4L. THIS LARGE ACFT ROTATED AND PASSED ABOVE ACR Y. WE WERE BEHIND ACR Y AND NEVER IN DANGER. ACR Y AVOIDED A CATASTROPHE. TWR WAS UNAWARE OF THE PROBLEM UNTIL ACR Y RPTED IT. THE CTLR IN THE TWR WAS EXTREMELY BUSY MONITORING ILS TO RWY 4R; CLRING VISUALS TO CONTINUE AND LAND ON RWY 29 AS WELL AS CROSSING RWY 4L. SUPPLEMENTAL INFO FROM ACN 545421: AFTER LNDG ON RWY 4R WE EXITED AT TXWY KILO AND CLRED THE RWY. HOLDING SHORT OF RWY 4L BEHIND A B737 AS INSTRUCTED BY THE TWR. WE WERE THEN CLRED TO CROSS; ALONG WITH THE B737; RWY 4L. THE B737 BEGAN TO CROSS RWY 4L AND THEN STOPPED; PARTIALLY ON THE RWY. AT THAT TIME WE NOTICED A LARGE; TRANSPORT CATEGORY JET ON TKOF ROLL ON RWY 4L. B737 ADVISED THE TWR OF THEIR POS AND THE ACFT ON RWY 4L CONTINUED ITS TKOF ROLL AND PASSED OVER THE B737. WE CONTINUED TO HOLD SHORT OF THE RWY AND WERE NEVER IN ANY JEOPARDY. HOWEVER; SINCE WE HAD ALSO BEEN CLRED TO CROSS RWY 4L WHILE AN ACFT WAS DEPARTING ON IT WE FELT THE NEED FOR THIS RPT. THE B737 CREW ACTED RESPONSIBLY AND AVOIDED A POTENTIAL DISASTER AS A RESULT OF THE TWR CTLR'S MISTAKE. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: CALLBACK REVEALED THAT THE LEAD B737 ENCROACHED BTWN 5 AND 20 FT ONTO THE RWY BEFORE APPARENTLY REALIZING THAT AN ACFT HAD BEEN CLRED FOR TKOF ON THAT RWY. THE DEPARTURE ACFT WAS BTWN 60 AND 200 FT IN THE AIR AS IT PASSED OVER THE LEAD B737. WHILE THERE WAS ONLY ONE LOCAL CTLR FOR BOTH DEPARTURES AND ARRIVALS NEITHER RPTR REMEMBERED HEARING THE TKOF CLRNC. THE ENVIRONMENTAL CONDITIONS AT THE TIME WERE NIGHT WITH LOW CLOUDS.