I understand, and that was a concern I had too, but unless you are with one of the few "sanctioned" tour companies (the ones who are actually approved by the Vatican and so they go early in the morning and do completely avoid the queues), no matter what "company" you go with, you will queue. If the only reason to do a tour is to queue (i.e. you don't care that much about the information the tour guide will provide), you might as well just save your money for gelato and pizza and go yourself, in the afternoon, and do it on your own (like with RS's guided tour in his book) or with the audio guide. Queue around 1, everyone says you won't have to wait nearly as long, stay in the museum/Sistene Chapel til it closes at 4:45pm, then go to St. Peter's for a couple hours since it is open later. You'll get to see it all, will have minimal queues, will not spend extra money on a tour, and you can do something else in the morning! :)