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In the last episode of season 6 we see what is clearly..
The truth about Jon's parentage, being the son of Lyanna Stark and Rhaegar Targaryen.
Without getting into the "why" and "if" about this, (It is already covered in many other questions on this site)
Would Jon Snow still be a bastard if people knew who his parents are?
Just to be clear, i am not asking if he has a claim to the Iron Throne or not.
People knowing who Jon's parents are does not mean anything for his bastard status. One is born a bastard if he is born out of wedlock, regardless to who the parents were.
Him being son of Lyanna and Rhaegar does not prove that they had married as well because Rhaegar was already married to Elia Martell and traditionally Westeros is a strictly monogamous region by faith and culture. Being a bastard of a Prince does not mean that someone becomes legitimate child. There are plenty of examples of Bastards sired by Targaryen Princes and Monarchs e.g. Daemon Blackfyre, Aegor Bittersteel, Brynden Bloodraven etc.
It is however entirely possible that Rhaegar may have married Lyanna following the precedent of Aegon the Conqeuror who had two wives. King Maegor also had multiple wives. Quoting GRRM:
[Questions concerning Targaryen polygamy.]
Maegor the Cruel has multiple wives, from lines outside his own, so there was and is precedent. However, the extent to which the Targaryen kings could defy convention, the Faith, and the opinions of the other lords decreased markedly after they no longer had dragons. If you have a dragon, you can have as many wives as you want, and people are less likely to object.
Simple answer is, from Season Finale, we do not know if they had married or not. Thus we cannot say if Jon would remain a bastard or not.
UPDATE: In Season 7, it is revealed that Rhaegar had his marriage to Elia annulled and married someone else. That someone else can only be Lyanna, making Jon a legitimate Child. So it is all but confirmed in the show that Jon is now a trueborn Targaryen.
From S07E05:
Gilly: What does "annulment" mean?
Sam: It's when a man sets aside his lawful wife.
Gilly: Maynard says here that he issued an annulment for a Prince "Ragger" and remarried him to someone else at the same time in a secret ceremony in Dorne. Is that a common thing in the south or--?
Robert would kill him, you know he will thing she said to Ned. There can be no plausible reason for Robert to kill Lyanna's son unless he was a Targaryen, I suppose. Why kill the infant if he is not blood of your rival and a possible threat to your throne?
As of S7E5 it appears that
Rhaegar had an annulment.
As was read by Gilly to Sam. However, the full passage was cut off.
[Gilly] What does ann-ull-ment mean?
[Sam] It's when a men sets aside his lawful wife.
[Gilly] Maynard says here that he issued an annulment for a Prince "Ragger" and remarried him to someone else at the same time in a secret ceremony in Dorne. Is that a common thing....
[Sam] Begins ranting about other things
So while we do not 100% know for sure if
It was Lyanna Stark that was the "someone else at the same time"... but who else would fit the bill of "a secret ceremony in Dorne"...
This would make Jon
a legitimate Targaryen based on most customs in Westeros.
