"No, that is totally untrue," Ryan said in a conference call with the Chicago media. "That was one of the biggest ... that's a joke. He wasn't that way at all."
Holmes spent four seasons with the Jets (2010-13) before signing in August with the Chicago Bears as a replacement for Marquess Wilson, who suffered a fractured clavicle during training camp. With the Jets, Holmes caught 146 passes for 2,168 yards and 16 touchdowns, but he came under fire toward the latter portion of his tenure after signing a five-year contract coming out of the NFL lockout in 2011 worth $45 million.
One New York Daily News report, citing anonymous sources back in January 2012, quoted a player saying Holmes is "a cancer. It's like dealing with a 10-year-old."
Former Jets running back LaDainian Tomlinson discussed a rift between Holmes and current Eagles backup quarterback Mark Sanchez on Showtime's "Inside the NFL" shortly after, saying, "It is as bad as I've ever been around, honestly."
Sanchez played for the Jets from 2009 to '13.
"In all seriousness, Santonio, obviously, he is a great player," Tomlinson said. "There are some things that obviously he needs to work on as far as being a leader."
Ryan, meanwhile, described his experience with Holmes as pleasant.
"I really enjoyed him," Ryan said. "When this guy's healthy, he can be a game-changer. The first year we had him, he was a major, major factor in us winning games. My second year here, he helped lead us to the championship game. He looks kind of funny in that [No.] 14 [Bears] jersey."
Shortly after joining the Bears, Holmes acknowledged some of the struggles he experienced with the Jets but also said he enjoyed playing there. Throughout his short tenure in Chicago, Holmes continues to work with receivers coach Mike Groh to learn the nuances of the club's offense while also serving as a mentor to some of the club's younger receivers.
In the locker room, Holmes has actually been one of the club's quieter players.
Receiver Brandon Marshall said "I love it" when asked about the acquisition of Holmes, while quarterback Jay Cutler said Holmes "can definitely still go. It's fun just trying to catch him up to speed."
As for Holmes, he's just excited "to embrace" his latest opportunity with the Bears.
Asked about his experience in New York, Holmes said, "It was great. I had a lot of fun. It was a great move by the organization of picking me up and giving me the opportunity to be the No. 1 guy. I made a lot of friends there, and we won a lot of ballgames."
Later in the day, Ryan acknowledged that he made a mistake by naming Holmes a captain in 2011. That year, Holmes clashed with teammates and was thrown out of the huddle late in the final game of the season. That prompted Ryan to abolish the tradition of appointing captains for the season.
"It might not have been a great selection," Ryan told New York reporters.
Ryan, reminded on the huddle incident, called it "an isolated case." For the most part, he praised Holmes, but he also recalled an incident in which the mercurial wide receiver publicly criticized the offensive line in 2011.
"Did he say something in the press that upset some teammates? Yes, but he's not the only guy that ever happened to," Ryan said. "I tell you, I think Tone meant well. Sometimes you don't necessarily see the big picture when you say something -- me or anybody else. He was trying to stand up for somebody and, at the same time, maybe he put somebody else under the bus. I've never done it like that, but these things happen sometimes. I never thought he was a bad teammate."
ESPN.com Jets reporter Rich Cimini contributed to this report.