Daenerys.
Also Roose is too kind for me, it's not a theroy I invented, but support. :b
TLDR Logic reasoning:
Ned Stark never cared too much for Jon Snow, but when he 1st enters King's Landing he begins to think about Rhaegar Targaryen (if Jon was Rhaegar's son, you would assume Ned would think about Rhaegar more) and Ned's downfall and his friendship split with Robert all circles around Ned's promise to Lyanna and making sure Daenerys isn't assisnated.
If Ned's feverish dreams about Lyanna's promise have him so determined to make sure Daenerys doesn't die, why would Lyanna's promise have anything to do with Jon and why would Jon be with the Night's Watch if Ned knew how important Jon is?
There just isn't that much real evidence that Jon is a Targaryen, just some prophecies about a Blue rose in the wall.