In the House of the Undying prophecy Rhaegar is described by Danaerys but the woman is not described. Could this be Lysnna Stark and Jon Snow instead of Elia Martell?
No. Rhaegar never saw Jon Snow alive, because he died at the Trident several months before Jon was born - since Ned was present at Jon's birth and had ridden all the way from King's Landing to the Tower of Joy to get there.
Moreover, we can use context clues and process of elimination to figure out who's who. Since Rhaegar says "there must be one more," and the baby is referred to as a "he," the child must be Aegon.
Which means the woman absolutely is Elia.
Rhaenys was born in 280 AC, probably towards the end of the year since Elia and Rhaegar were married that same year. Elia was bedridden for six months after giving birth to Rhaenys, so Aegon's date of conception was probably at least three months into 281, which doesn't leave much time for Aegon to have been born at the end of 281/very beginning of 282.
Aegon's birth nearly killed Elia and rendered her infertile; it is extremely unlikely that Elia would have allowed Lyanna Stark anywhere near her precious "newborn" son (or been in condition to receive her) so soon after her humiliation at the Tourney of Harrenhal. Moreover, we know that around that time of just after the New Year of 282, Rhaegar unexpectedly left his wife and newborn son behind on Dragonstone and took to the road with his companions, riding back to the Riverlands to the area near Harrenhal where he rendezvoused with Lyanna.
Finally, it's just not credible that Lyanna could have made a secret trip from Riverrun to Dragonstone and back to Riverrun without anyone noticing. Given that Lyanna was almost certainly at Riverrun getting ready for her brother's wedding, there would have been people at the castle who would have seen her comings and goings - as in fact was the case when she did rendezvous with Rhaegar, and Brandon found out about it.
