The surprise selection sees the likes of Cristiano Ronaldo, Paul Scholes and Ryan Giggs miss out on claiming top spot on Howard's personal list.
While Keane may not have the skill of Ronaldo, Howard was left in awe of the Irishman's ferocity and he ultimately had a meaningful influence over the former Everton shot-stopper's career.
"I played with so many great players and leaders in my career, but to me, none was better than Roy Keane during my time at Manchester," Howard wrote in a column for ESPN.
"He was the toughest son of a b*tch I ever met. Nothing short of brilliant.
"As a coach, he taught me about resilience. And never giving up on myself. I took so much of what I learned from being around him and used it over the rest of my career, trying to pass it along to the next generation."
After struggling to cement himself at Old Trafford, Howard moved to Everton on loan in 2006 before signing with the Toffees permanently.
Looking back on his career, the American recalled the good times at Goodison Park and highlighted one particularly fiery incident involving coach David Moyes.
"There are so many other good things I will forever take with me. The day I wore the captain's band for Everton when we played at Chelsea. Or the day David Moyes taught me what the term spitting mad truly meant," Howard wrote.
"After I had a terrible game, he looked at me with such disappointment and just started screaming and yelling.
"I could barely get my eyes off the floor. I'm looking down and all this spit was flying all over the floor, and I remember thinking, 'So that's what it means to be spitting mad'."
The life of a goalkeeper wasn't always easy for Howard, but he admits all the heartache was worth it in the end.
"If I could go back to 2003 and that nervous, naive 24-year-old kid on a plane flying to England to play for Manchester United, about to sign with the biggest football club in the world, I'd tell him to buckle up tight. It's going to be one hell of a ride," he wrote.
"There will be good days and bad. You're going to go to some dark places. You're going to wonder if you should give up. People will criticise you for decades on end. But it will all be worth it."