John:

We used a company called Scala Reale; now known as context rome. Here is the link to their site.

They have a series of walking tours given by art and architecture experts. We took four tours. Ancient Rome, Vatican, nighttime tour of central rome, and Villa Borghese. All tours are limited to six people. The Villa Borghese tour was booked as a private tour but we ended up inviting some folks from our Vatican tour to join us. All were absolutely fantastic. I see that they now have many more options for tours.

We strongly recommend them; especially for the Vatican. Also recommend you set up a tour directly with the Vatican to see the tombs underneath St. Peter's.