With the Islanders trailing 3-1 late in the second period, New York got a five-minute advantage after Michael Ryder was whistled for slamming New York's Blake Comeau into the end boards. Comeau was taken off the ice on a stretcher and Ryder was given a major penalty and a game misconduct.
But Thomas shut the door during the man-advantage, which stretched from the second into the third period. Matt Moulson's goal pulled New York to within 3-2 with less than six minutes left, but the Islanders couldn't dent the Bruins' netminder the rest of the way.
Milan Lucic, David Krejci and Marc Savard tallied for Boston, winners of five of its last six games.
Josh Bailey got the Islanders' other goal while Dwayne Roloson lost despite a 31-save performance.