The ad was in the form of an open letter signed by Blackhawks Chairman Rocky Wirtz, and by President and Chief Executive Officer John McDonough, the Chicago Tribune reported.
The ad ran Friday -- the same day about 2 million fans turned out in Chicago for the Blackhawks' victory parade.
"Hockey is a tough game. As impressed as we were by the strength, talent and competitive spirit of the Boston Bruins on the ice, we were deeply touched by what happened off the ice," the ad said. "Rarely have we experienced the hospitality you afforded us throughout the playoff series between two incredibly gifted teams."
The ad referred to the bombings during the Boston Marathon on April 15.
"Please know we tip our hat to your city's big heart and gracious spirit," it read. "You lead by example and have set the bar very high for others to follow."