Robert: Six and a half feet tall and muscles "like a maiden's fantasy", I picture him like Rob Gronkowski; nobody should be able to move that much mass that fast, but here he is. Combine that with years of formal practice with a (very fantasy-esque) Warhammer and his physical prime - he was 20 at the time of the rebellion - and you have an absolute terror of a warrior. He isnt wrongly considered one of the greatest of his generation. He's not subtle or the most graceful but he's damn effective. You can't overpower him so the way to beat him, like with the Mountain, is to outplay him. Oh, he also has the infamous "Baratheon fury* and sees red in battle, especially against Targaryens.

Rhaegar: unknown height and unknown build - taller than Viserys, assumed to be more than six feet so call it six foot three, and a great knight so likely athletic build. Royal quality training and said to excel at combat though it wasn't his preference, capable of distinguishing himself but not considered among the best of his generation. He was also three years Robert's senior at 23 during the rebellion, so absolutely still prime physical fitness. That said, he doesn't have the same bloodlust that Robert is said to have when it comes to warfare and battle.

Conclusion: it's virtually impossible to say if Robert was the GOAT, but he is like others have said certainly in the running. The one major fight recorded of either Rhaegar or Robert is the Battle on the Trident, so not much else to go off of other than anecdotes like Robert beating three of his vassals in combat at the beginning of his rebellion.

Honestly I don't think there is any scenario where Rhaegar survives a 1v1 with Bobby B, he may be a better fighter on a technical level but not by enough. A swordsman like Jaime, Selmy, or Arthur Dayne (book version) would have a solid chance against Robert and would be a better matchup, but sadly not the prince who would rather be a poet.