To go back to my earlier question about Howland Reed, it seems like Jon and Meera are the easiest secret Targaryens to explain.
Bran shows up and has a vision of Tower of Joy, and then Howland Reed shows up and says, "Yep, these two are twins of Rhaegar and Lyanna."
Other than a Bran vision who would know and back up that Tyrion is a Targaryen? Is he just supposed to get on a dragon and everyone agree that must be what it means?
Also, Meera as the other one matches up the current riders to the historical ones, 1 male and two females.
On Tyrion...
It is easy to write it into the current story.
-It could be a Bran vision (as you say)
-someone could come across a hidden written account of the true story (maybe at Casterly Rock).
-Jaime and/or Cersei might reveal that he/she (both) have known the truth all along but did not want to share it to protect the family from embarrassment.
On Meera...
I agree that it would fit better. They have already set the stage for the 2nd half of the Tower of Joy scene. We all know that we will see it at some point. Howland Reed might or might not show up to confirm the story. Benjen is back and might know the truth (told by Ned).
On Jon....
I think we all agree that R+L= J. I am now expecting Dani and the dragons to end up in the North fairly quickly. That should set the stage for him to end up on a Dragon's back while it is burning the WW and Zombie army.