Stoudermire, who sat out part of the NBA playoffs last month after he cut his left hand punching a glass-enclosed fire extinguisher, called a fan a gay slur on Twitter Saturday during Gay Pride Weekend.
The NBA is reportedly investigating the incident and the message's authenticity.
The incident happened after Twitter user and Knicks fan BFerrelli, identified in news reports as Brian Ferrelli, posted a message for Stoudemire telling him: "you better come back a lot stronger and quicker to make up for this past season mannnnnn deadasss!!!"
Stoudemire reportedly replied to Ferrelli in a direct message — which, unlike a normal Twitter post, can only be read by the recipient — firing off the offending language.
"F--k you. I don't have to do any thing f--," Stoudemire responded.
Ferrelli then took a snapshot of the message and sent it to sports news and gossip website Deadspin.com.
The message and its timeliness sparked an online frenzy, and the following morning Deadspin reported that Stoudemire apologized to Ferrelli via direct message — with Ferrelli again sending the note to the sports website.
"I apologize for what I said earlier.I just got off the plane and had time to think about it. Sorry bro!! No Excuses. Won't happen again," Stoudemire reportedly wrote.
Ferrelli, who sports tattoos, a tank top shirt, and a pair of earrings in his Twitter photo, said he hopes to put the exchange behind him.
"I don't want to make this situation any bigger than it already is. He apologized and I accepted it," he told the Daily News in a Tweet.
It was unclear Monday whether the NBA would take action against Stoudemire. In 2011, Los Angeles Lakers All-Star Kobe Bryant was fined $100,000 for calling a referee the same homophobic slur during an April 10 game against San Antonio.