As others have said, there's no canon information on where she got the names.
However, it's worth noting that Anakin probably hadn't agreed upon those names at any point--by the end of TESB he's aware that Luke's his son, but (in the special edition) the Emperor says he has no doubt that Luke is "the son of Anakin Skywalker", and Vader asks how it's possible. It's a strange line to begin with, but it's even stranger if he didn't put two and two together the moment he first heard of someone with his last name and the first name he came up with, who's roughly as old as the last time he saw Padme alive. Add in the fact that Luke is a known associate of Leia, who is publicly known to be adopted and (under the theory) has the first name he chose, and it gets even less plausible that he'd take so long to figure it out if he had any input on the names.
Even in the (now-Legends) Expanded Universe, when Vader finds out the identity of the pilot who destroyed the Death Star from multiple sources (one of which is in the comic miniseries Vader's Quest, from a captured Rebel), it's the "Skywalker" part he's paying most attention to, implying that the "Luke" part isn't particularly meaningful. (Yes, some of these sources came out before the prequels, but The Rise and Fall of Darth Vader came out afterward and referenced most of the sources, still without mentioning any significance to "Luke" throughout.)
Personally, I like the idea that they're traditional Naboo names that Padme never got the chance to ask Anakin about, but that's just speculation/fanon.