Journalist Tom English wrote in Scotland on Sunday it was not good for Celtic that one of its players would have such close links to Ryan.
Stokes knew Ryan (32) for years through the RIRA man's association with the Players' Lounge Bar in Fairview, which is owned by the footballer's family.
The 24-year-old striker was at a memorial in Crumlin for Ryan, who was shot dead near his home on September 3 last in Donaghmede.
Stokes took to Twitter, saying: "Nice article this morning, so many lies."
The journalist hit back, telling the footballer: "I did my homework just fine, Anthony. If I got facts wrong then feel free to sue me."
Stokes told him he has "already arranged for that".
But Mr English responded: "Good for you. You might be surprised to see who some of my witnesses are going to be."
The spat erupted in the wake of the article which was heavily critical of Stokes' links to Ryan. Stokes, who is currently out through injury, told the journalist he knew Alan through the pub and he was not a childhood friend.
Mr English reported that Celtic said they take a very dim view of Stokes' attendance at the benefit night in Crumlin and that they will deal with it internally.
Hundreds of people attended the November 2 memorial for Ryan at the Submarine Bar which was closely watched by armed gardai.
Photographs later emerged of Stokes enjoying himself at the event.
The footballer said he was "attending a fundraiser for a family to pay funeral costs".
During the night, friends of the murdered criminal joined together to sing The Ballad Of Alan Ryan -- which vows to avenge his killers.
Gardai believe Ryan was responsible for a number of murders, including the shooting dead of criminal Sean Winters in Portmarnock in September 2010 and the gunning down of gangland figure Michael 'Mica' Kelly in north Dublin in September last year.
As Ryan was laid to rest, a volley of shots was fired over Ryan's coffin as he was given a full republican military funeral.