Well, if there was an annulment of Rhaegar's marriage to Elia Martell, and he subsequently married Lyanna Stark, then I would think that Jon Snow would be the legitimate heir to the Iron Throne. Now, two weeks ago, I would have said no to that proposition, because, as far as I knew, Lyanna & Rhaegar were not married. But, if they were legally married, he having gotten rid of his first wife, then I think Jon does have a claim to the throne.
Bigger question: Would Jon want the Iron Throne?
Bigger question, if true will Danerys bend the knee to John Snow?