Noboyuki Shirota, also from Japan, came in second after wolfing down 38 hot dogs.
Sonya "The Black Widow" Thomas, came in third with 32 dogs, breaking the women's world record.
"She's just beginning with this, so the sky's the limit," Mr Shea said of Sonya's efforts.
The hot dog competition has been running at Coney island since 1916.
Around 3,000 people went to watch the contest.