SMA HAS NMAC WHILE OVERFLYING TCA.

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CRUISING AT 7500 FT OVER THE BOSTON TCA ON A COURSE OF APPROX 015-020 ENRTE TO SFM VIA BEDFORD/LWM. WE HAD DEPARTED OCEAN ARSA AND WERE ADVISED THAT A HDOF TO BOSTON APCH COULD NOT BE ACCOMPLISHED BUT WERE ADVISED TO CONTACT BOSTON APCH DIRECTLY. WE DID THIS AND HAD INITIAL DIFFICULTY WITH OUR #1 RADIO REACHING BOSTON AND COULD NOT EASILY UNDERSTAND THE SQUAWK CODE. WE WERE ADVISED THAT OUR TRANSPONDER WAS NOT WORKING AND NOT TO ENTER THE BOSTON TCA. TRANSPONDER TESTING LIGHT AND SWEEP PERIODICALLY TURNED THE TRANSPONDER ON IN ANY EVENT APPROX 3-5 MINS WAS SPENT DEALING WITH THIS PROBLEM. I FINALLY TRIED THE #2 RADIO AND ESTABLISHED CLR COMS WITH BOSTON TCA S OF THE FIELD AND WAS STILL ADVISED THAT OUR TRANSPONDER WAS NOT OPERATING. AROUND THIS TIME WE OBSERVED AN SMA Y; WHITE WITH YELLOW AND BLUE TRIM AT OUR ALT HDG APPROX W OR SW AT 7500 FT MAKE AN ABRUPT TURN TO THE S TO ASSURE MISSING OUR ACFT. I JUST SAW THE SMA Y AS IT TURNED AND FROM THE DIRECTION OF THE TURN WAS ABLE TO DETERMINE ITS COURSE OF FLT. AS TO THE CAUSE OF THE NEAR MISS OF APPROX 300 FT HORIZ; MY FIRST AND PRIMARY CAUSE WOULD BE THE SMA Y TRAVELING WBOUND AT 7500 FT. SECONDARILY; IF WE HAD HAD FLT FOLLOWING I PRESUME WE WOULD HAVE BEEN ADVISED OF THE PRESENCE OF ANOTHER ACFT IN OUR VICINITY. NOT A WORD WAS STATED ON THE RADIO AFTER THE INCIDENT BY THE SMA Y OR US OR THE CTLR. MIRACULOUSLY; AFTER THE INCIDENT OUR TRANSPONDER STARTED TO WORK AGAIN WHEN WE CONTACTED BOSTON APCH N OF THE FIELD. THE STAFF AT THE FBO STATED TO ME THAT THIS WAS A COMMON OCCURRENCE TO LOSE TRANSPONDER AND THEN REGAIN IT AFTER LEAVING THE BOSTON TCA AREA IF THE AREA WAS BUSY.