Gendry came to work for Tobho Mott when an unnamed Lord paid him to take him on as an apprentice. This lord would have known who Gendry was too as he paid double with the second fee being for Tobho to keep his mouth shut.

Ned touched the boy's head, fingering the thick black hair. "Look at me, Gendry." The apprentice lifted his face. Ned studied the shape of his jaw, the eyes like blue ice. Yes, he thought, I see it. "Go back to your work, lad. I'm sorry to have bothered you." He walked back to the house with the master. "Who paid the boy's apprentice fee?" he asked lightly.
Mott looked fretful. "You saw the boy. Such a strong boy. Those hands of his, those hands were made for hammers. He had such promise, I took him on without a fee."
"The truth now," Ned urged. "The streets are full of strong boys. The day you take on an apprentice without a fee will be the day the Wall comes down. Who paid for him?"
"A lord," the master said reluctantly. "He gave no name, and wore no sigil on his coat. He paid in gold, twice the customary sum, and said he was paying once for the boy, and once for my silence."
"Describe him."
"He was stout, round of shoulder, not so tall as you. Brown beard, but there was a bit of red in it, I'll swear. He wore a rich cloak, that I do remember, heavy purple velvet worked with silver threads, but the hood shadowed his face and I never did see him clear." He hesitated a moment. "My lord, I want no trouble."
_{A Game of Thrones, Eddard VI}

Gendry came to work for Tobho Mott when an unnamed Lord paid him to take him on as an apprentice. This lord would have known who Gendry was too as he paid double with the second fee being for Tobho to keep his mouth shut.

Ned touched the boy's head, fingering the thick black hair. "Look at me, Gendry." The apprentice lifted his face. Ned studied the shape of his jaw, the eyes like blue ice. Yes, he thought, I see it. "Go back to your work, lad. I'm sorry to have bothered you." He walked back to the house with the master. "Who paid the boy's apprentice fee?" he asked lightly.
Mott looked fretful. "You saw the boy. Such a strong boy. Those hands of his, those hands were made for hammers. He had such promise, I took him on without a fee."
"The truth now," Ned urged. "The streets are full of strong boys. The day you take on an apprentice without a fee will be the day the Wall comes down. Who paid for him?"
"A lord," the master said reluctantly. "He gave no name, and wore no sigil on his coat. He paid in gold, twice the customary sum, and said he was paying once for the boy, and once for my silence."
"Describe him."
"He was stout, round of shoulder, not so tall as you. Brown beard, but there was a bit of red in it, I'll swear. He wore a rich cloak, that I do remember, heavy purple velvet worked with silver threads, but the hood shadowed his face and I never did see him clear." He hesitated a moment. "My lord, I want no trouble."
_{A Game of Thrones, Eddard VI}

As for who the lord was that paid the fee well we don't know. I believe though that the leading theory is that it was Varys in a disguise. He clearly knows about them as he remarks to Tyrion.

"Robert's bastards? What of them?"
"He fathered eight, to the best of my knowing," Varys said as he wrestled with the saddle. "Their mothers were copper and honey, chestnut and butter, yet the babes were all black as ravens . . . and as ill-omened, it would seem. So when Joffrey, Myrcella, and Tommen slid out between your sister's thighs, each as golden as the sun, the truth was not hard to glimpse."
_{A Clash of Kings, Tyrion III}

We know he likes to use disguises too as is evident when again he tells Tyrion.

"The work I do does not permit me to travel the streets amid a column of knights. So when I leave the castle, I adopt more suitable guises, and thus live to serve you longer."
_ibid