Actually, we are 100% sure that it is the grave site (or at least as close to 100% as you can be 2000 years later). The skepticism is instead placed upon the remains found there. Tradition states that the tomb has always been there. When they did the excavations, they found a tomb inset into a small shrine which exactly matches contemporary descriptions of Peter’s tomb. The center stone was broken and the full inscription was lost, but this too aligns with history. In the early 3rd century, a decree was made by the Emperor for the purpose of discouraging Christian veneration of the Saints. It stated that it was illegal for non-cremated remains to be kept within the boundaries of the city. The Pope ordered the tombs of Sts. Peter and Paul to be opened and their remains removed for fear that the Romans would destroy them. If you look closely, the stone which covered the tomb of St. Paul was also broken at this time. The remains were taken to the Catacomb of St. Sebastian and remained there until a small shrine (which was found in the excavations around the Catacomb) was built among the pagan tombs along the Via Ostiensis to camouflage it from Romans who wished to destroy it. It wasn’t until Constantine commissioned the Lateran, St. Peter’s and St. Paul’s Basilicas that they were moved back. Because the remains of Peter and Paul had been together for a period of time and local tradition united their devotion, the heads of Peter and Paul were kept together and brought to San Giovanni in Laterno (Lateran Basilica) where they still reside in reliquaries above the altar. St. Paul’s body was replaced in his tomb and it was bricked over. St. Peter’s remains were not replaced, however, as the tomb itself was too damaged, so they were placed in a niche above the tomb and it was enclosed to make the altar for the new Basilica. The skepticism about the remains comes from whether or not we found the right box of bones and if it wasn’t lost when they rebuilt St. Peter’s starting in the 1400’s as Bramante, the original architect of the new St. Perers, was of the mindset of “Tear everything down, throw it away, and start from scratch.”
