Judge, who had gone homerless in seven games, crushed a two-run homer in the seventh inning in Wednesday's game against the Toronto Blue Jays.
Judge's record-tying 61st home run comes with another seven games remaining in the regular season. Maris' mark dates back to 1961, edging Babe Ruth's previous record of 60 in 1927.
"It's an incredible honour, getting a chance to be associated with one of the Yankee greats, one of baseball's greats, words can't describe it," Judge said.
"That's one thing so special about the Yankees organisation, is all the guys that came before us and kind of paved the way and played the game the right way, did things the right way, did a lot of great things in this game and getting a chance to be mentioned with those guys now is, I can't even describe it, it's an incredible honor that's for sure."
The 30-year-old had gone 31 consecutive homerless plate appearances coming into Wednesday's game with some speculation he may be rested with the Yankees clinching the AL East on Tuesday.
Only three players have scored more homers in a single season for any franchise than Judge; Barry Bonds (73 in 2001), Mark McGwire (70 in 1999 and 65 in 1999) and Sammy Sosa (66 in 1998, 64 in 2001, 63 in 1999). Those three players all achieved the feat during the steroid era.
"I think it puts it a notch above," Boone said about Judge last week. "I got to believe it's right there with some of the best very short list of all-time seasons. I go back to the context of the season, and the more I look at it and dive into it, it's got to be an all-time great season."