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To the south of the present basilica, extending eastward into the current piazza, was the Circus of Nero, where St. Peter was crucified. North of that, where the basilica itself now sits, was a pagan cemetery. Peter was buried on the west edge of that cemetery. A disguised shrine - the Tropaion - was built over this spot in the early 2nd Century. And, of course, the high altar of the original St. Peter's basilica was built over that in the 4th Century.

All of this, from an archaeological POV, was rediscovered during the preparations for Pius XI's gravesite in 1939, when the lower church floor was breached for the grave, and the walls of what turned-out to be a pagan tomb were revealed after some digging.

Long story short, the archaeologists were called in, and it was realized that the ancient pagan cemetery long-believed to be under the church was a fact. Over the course of the next ten years or so, Pius XII gave permission for excavations to proceed under the basilica westward toward the traditional site of Peter's grave. Pagan mausoleums and grave became mixed with Christian ones, the closer one got to the traditional spot. A grave with fairly conclusive clues regarding St. Peter was found, with a multitude of Latin inscriptions carved by 4th Century pilgrims present on an adjoining support wall. The site was directly under the main altar of both the current basilica and the known location of the Constantinian one!

I got most of this from a book I purchased and read the very day I took the tour under the basilica (highly recommended if you're ever in Rome! Just set it up at the tour office run by the Swiss Guards on the south (left) side of the Basilica.), called "The Bones of St. Peter," By John Walsh. This book is available from Amazon, of course, but it is also available right here: http://saintpetersbasilica.org/Necropolis/JW/TheBonesofStPeter-1.htm , complete with the original book's pictures! You might want to check it out...