The surprising thing about the statement that Tom had "a cruel body" is that Nick was friends with him. Although Nick clarifies that Tom and Daisy were "two old friends" whom he barely knew, the way he describes Tom is with a tone more akin to dislike or hostility than friendship. Even through the eyes of a friend, Tom is undeniably overbearing and intimidating, which hardly bodes well for the character and the audience's perception of him. 

A few lines before Nick describes Tom's body as cruel, he says that "two shining arrogant eyes had established dominance over his face and gave him the appearance of always leaning aggressively forward." He also states that Tom had a "rather hard mouth" and, later on, a "great pack of muscle shifting when his shoulder moved."  It's not just Tom's posture or his attitude that makes him appear menacing and distinctly unlikable, but it's quite literally the product of even his most minute features. 

And all this description comes from Nick Carraway, a man who in the very first lines of the book clarifies that he tries his best not to judge people.

"I’m inclined to reserve all judgments..."

Tom Buchanan is described as having a "cruel body".  He says this in the first chapter of the book when Nick is describing Tom for the first time.  Nick says that Tom's body was "...capable of enormous leverage - a cruel body."  He means that Tom uses his physical size to intimidate and bully people.  Tom is used to getting his way in matters and since he is immature and selfish, this means sometimes using force.