In an Alternative Universe when everyone knew Jon was a Targaryen + the Targaryens still were sitting on the Iron Throne, who was in the first line to rule next? Jon or Daenerys?

Jon probably. Aerys was the king, Rhaegar was the crown prince so Rhaegar's son would come susunod in the line and since Aegon is dead, that puts Jon susunod in line for the throne. But Jon's claim could be weaker if Rhaegar and Lyanna weren't married.

So in short, Jon is the heir to the Iron trono if Rhaegar and Lyanna were married. If not, then Jon is still a bastard with a weak claim and Daenerys has a stronger claim.

Jon would be susunod in line if his parents did marry or if he was legitimised sa pamamagitan ng the king. A legitimate child comes before a sibling - siblings are only heirs if someone has no children/only bastards.