You can try www.welwalkinrome.com - they have daily Vatican tours at 2pm. I sisn't do this one, though, I did their Ancient Rome tour and found it BRILLIANT. They are a small Italian company (only 3 or 4 guides in total) and I am sure their other tours are of excellenty quality also.
However, if your aim of a tour is only to avoid entrance lines, then try taking Rick's tip of going Wednesday morning after 10am when the Pope is giving his public audience and everyone is heading to St. Peter's. I did this two weeks ago, and it was amazing - no lines at all, we were in the Museum within 5 minutes of getting there!