Let's look at the suspension histories of both teams:
2013-2014 Bruins: Shawn Thornton: Pending
2013-2014 Pens: James Neal: Pending
2013 Bruins: Andrew Ference: May 2, 1 game suspension
2013 Pens: N/A
2011-2012 Bruins: Andrew Ference, January 22, 3 game suspension
Brad Marchand, January 9, 5 game suspension
Milan Lucic, December 19, 1 game suspension
2011-2012 Pens: Arron Asham, April 17, 4 game suspension
James Neal, April 17, 1 game suspension
Craig Adams, April 16, 1 game suspension
Deryk Engelland, December 22, 3 game suspension
Kris Letang, October 11, 2 game suspension
2010-2011 Bruins: 6 total games in suspensions
2010-2011 Pens: 24 total games in suspensions, plus the first round of the playoffs
2009-2010 Bruins: N/A
2009-2010 Pens: 2 total games in suspension
Based on suspension numbers alone, a Pittsburgh player has been suspended 37 games since the 2009-2010 season. In the same time span, a Boston player has been suspended 16 games.
It's pretty difficult to say that they're one of the cleanest in the league. Pittsburgh is certainly one of the dirtiest based on the suspension numbers alone. But Boston still has a high number of suspensions as well. Not many teams have double digits in suspended games.