Goodell discussed the issue during an interview with Allon Sinai of the Jerusalem Post.
"Robert is very important to me personally," he said. "My friendship with Robert was never strained. We both understand that we have jobs."
Kraft and Goodell are in Jerusalem for the opening of the Kraft Family Sports Complex.
Goodell added: "I know how important this is for him. My respect and admiration for him has never waned. We believe our best days are ahead."
It's a different tune than the one brought forward by Kraft ahead of last season's Super Bowl. In late January, Gary Myers of the New York Daily News passed along the Pats owner's response when asked about his relationship with the commish.
"I don't know if it will ever be the same, but in order to do what is best for the Patriots franchise long term, I believe it is best to compartmentalize and move on," he said. "Like our quarterback, I am trying to remain positive and look to the future rather than dwell on the past. As a native New Englander, that's easier said than done, but I am doing my best to put the matter behind me."
Those remarks came after Kraft reacted strongly to the NFL's investigation and subsequent punishment for Deflategate, which dates to the 2014 AFC Championship Game. The penalty included a four-game suspension for superstar quarterback Tom Brady.
He released a statement last July after Brady opted to discontinue the legal process into the matter, calling the penalties "unprecedented, unjust and unreasonable."
"While I was disappointed with the 2nd U.S. Circuit Court of Appeals' decision not to rehear Tom Brady's case, I am most frustrated that Tom was denied his right to a fair and impartial process," Kraft said. "The league's investigation into a football pressure matter was flawed and biased from the start, and has been discredited nearly unanimously by accredited academics and scientists."
Perhaps it's an example of winning healing all wounds, though. Brady returned from his suspension to have one of the best seasons of his career, and the Patriots capped the campaign with a comeback from 28-3 down to beat the Atlanta Falcons in Super Bowl LI.