B737-200 CREW AND EMBRAER HAD A CLOSE ENCOUNTER WHILE TAXIING AT BOS.

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AFTER AN EARLY EVENING LNDG ON RWY 27 AT BOS; I EXITED THE RWY AT HIGH SPD TXWY E AND WAS TOLD TO HOLD SHORT OF RWY 22L. OUTSIDE CONDITIONS WERE LATE DUSK (ALMOST NO SUNLIGHT) AND CLR SKIES. AFTER HOLDING SHORT OF RWY 22L FOR APPROX 3 SECONDS; TWR INSTRUCTED US TO CROSS RWY 22L AND HOLD SHORT OF RWY 22R; GIVE WAY TO AN EMBRAER. AS I CROSSED RWY 22L; I NOTICED AN ACFT AHEAD OF US ON TXWY E TOWARD RWY 22R HOLD SHORT LINE. IT WAS DARK AND TYPE OF ACFT WAS NOT EASILY DISTINGUISHED. IT WAS A COMMUTER PLANE. I ASSUMED THE ACFT WAS THE EMBRAER JET; SO I CONCENTRATED ON CLRING THE RWY 22L HOLD SHORT LINES TO BE CLR OF AN ACTIVE RWY. MY FO RPTED NO OTHER ACFT IN HIS SIGHT EXCEPT THE PREVIOUSLY MENTIONED ACFT. AS I CLRED THE RWY 22L HOLD SHORT LINE; THE TWR INSTRUCTED ME TO 'STOP.' I DID SO AND WAS TOLD THE EMBRAER WAS OFF OUR R. THE ACFT WAS APCHING FROM OUR R REAR BLIND SPOT ON TXWY P AFTER LNDG ON RWY 22L. HE STOPPED SHORT OF TXWY E AFTER NOTICING OUR ACFT NOT GIVING WAY. BOTH MY FO AND I DID NOT SEE HIM AND BOTH INCORRECTLY IDENTED THE ACFT AHEAD AS OUR TFC. ACFT CLRNC WAS APPROX 50 FT AT THE CLOSEST POINT. THE TWR INSTRUCTED US TO CONTINUE TAXI AND NO FURTHER INCIDENTS OCCURRED. FACTORS CONTRIBUTING TO THIS EVENT WERE ATC ISSUING UNCLR INSTRUCTIONS AS TO WHERE THE ACFT WAS COMING FROM AND DURING A HIGH WORKLOAD TIME FOR CREW; FAILURE OF CREW TO ASK FOR CLARIFICATION OF TFC'S POS; NIGHT VISIBILITY CONDITIONS; USE OF MULTIPLE FREQS FOR ACFT IN CLOSE PROX (JET WAS ON OTHER FREQ); AND CAPT'S CONCENTRATION ON XING ACTIVE RWY ASAP WHEN ISSUED XING INSTRUCTIONS.