With Arthur Dayne, Oswell Whent and the Captain of the Kingsguard Gerold Hightower protecting Lyanna in the Tower of Joy it is undisputed that Jon is the son of Rhaegar and Lyanna. Dayne being the finest swordsman there was and Gerold being there I would rip my hair out if he wasn't R+L=J. My assumption is that they were married on the Isle of Faces, the only place in the south with a godswood that Lyanna would marry at. Plus if you watch the Sean Bean interview about being question about Jon's parentage he flat out says Jon isn't his son. The only other possibility of Jon's parentage would be between Benjen Stark and Ashara Dayne, but that's another rant.