John Tavares netted the game-winner late in the 2, on Saturday.
Matt Moulson had a goal and an assist and Josh Bailey also lit the lamp for the Islanders, who snapped a three-game losing streak. Evgeni Nabokov made 32 saves in the win. Frans Nielsen added a pair of assists.
Milan Lucic and Tyler Seguin tallied for Boston, which has lost five of its last eight games.
On the game-winner, Moulson flew up the right wing and stopped before letting go of a slap shot from the right point. Tavares, stationed in front of Thomas, tipped it home with 4:39 to play.
The Bruins struck first late in the first period as Lucic snapped one into the back of the net from the slot on the power play 15:10 into the game.
New York, though, tied the contest just 2:26 later. Nielsen skated down the left wing and maneuvered into the right circle before feeding Bailey in the slot with a beautiful backhanded pass.
Moulson's power-play tally from the crease gave the Islanders a 2-1 lead late in the second.
The Bruins tied the game at the 7:29 mark of the third. Zdeno Chara led Seguin with a perfect bank pass along the right boards. Seguin flew in along the right side before lifting his backhander past Nabokov from the slot.
Boston has gone 10-11-2 over its last 22 contests and fell to 19-12-2 as the host this season...The Isles snapped a five-game road losing streak and moved to 13-15-4 away from home this year.