With the score tied at 3-3, Stepan made his way through traffic and beat Boston goalie Tim Thomas over his right arm for a Rangers lead with less than 8 minutes remaining in the final frame.
Carl Hagelin, Marian Gaborik and also scored as New York took its fourth win in five games and moved past Vancouver for the NHL's best record at 91 points.
Henrik Lundqvist notched his 31st win with 30 saves for the Rangers.
Thomas, meanwhile, let in four goals on just 17 shots for the Northeast Division-leading Bruins, who lost for the third time in four games.
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