Is there a new tour something underneath St Peter's?
The Scavi (excavations) tour has been around for quite awhile. You have to book it via e-mail directly with the Vatican. The tour guides are mostly Archeology students and they take you down under St. Peters to see the original Greek grave yards, the foundations of the original church and the wall where St. Peter's bones are believed to be. It's really interesting and definitely worth it. You can get the details under the Information section of the Vatican website (www.vatican.va). Just scroll down to the Visits to the Vatican Necropolis and click on Excavations office.
The Scavi is not that old but it is very interesting. The excavations began with work to prepare a burial place for Pope Pius XI (I think) when remains of the old Roman graveyard next to the Circus of Caligula and Nero were exposed. The Pope ordered extensive excavations that carried on for many years as old Roman tombs and Christian ones were revealed. It was during those excavations that artifacts that may be Peter's bones and ossuary were found. Whether on not it is indeed Peter's bones it is a fascinating excavation. Most of the guides are clerical students from various disciplines and young priests, some from the US. Some tours are given in English but not many. The office has been run for years by an old priest who admits he does not like Americans and tourists. They often create original impediments to taking the tours (you are too tall, you are not Catholic, no English tours this week, etc.) You might do better to have your hotel schedule your tour in Italian.