Moloney, 38, has called time on a distinguished career after he failed to recover from a shoulder injury he sustained in a fall at Sedgefield in January.
He is to return to his native Ireland to set up a breeding operation.
Geraghty, currently on the sidelines with a broken arm, tweeted: "The best of luck to Paul Moloney in his retirement we will miss him in the weighroom and watching him win on horses that never should have."
Champion jockey Johnson said Moloney's retirement was "a big loss to the weighing room".
He tweeted: "Very sad to hear of Paul Moloney's retirement, brilliant jockey and great man."
Moloney spent most of his riding days attached to Evan Williams' Welsh stable.
They had their first big-race success with State Of Play in the 2006 Hennessy Gold Cup and went on to enjoy other notable victories with horses like Deep Purple, Barizan, Court Minstrel and Buywise.
They also combined to finish in the first four in five consecutive Grand Nationals from 2009-13 with State Of Play and Cappa Bleu.
Moloney went on to achieve two further fourth-place finishes in the Grand National aboard Alvarado in 2014-15.
Williams said: "It's a big blow to the yard because he's been such a wonderful man to work with.
"We both found each other at the right time of our careers. I was starting and he was coming over from Ireland.
"We had a wonderful working relationship and some great days.
"I've enjoyed every single second working with him. We're all behind his retirement because it's the right thing for him and his family.
"Fingers crossed he can get on with the rest of his life and we've got so many happy memories. He was such a pleasure to work with."
Jockey Sam Twiston-Davies described Moloney as an "absolute genius on the back of a horse", while Aidan Coleman said he was a "great jockey and great man".
Tom Scudamore said: "All the best to this top gentleman. Been a pleasure to ride with him. Admired him enormously."
