Done Rome few times with Thomson,There is usually 3 tours.
Rome inc Vatican + lunch...£80
Rome staying on coach...£40 ish
Rome shuttle coach,drops off at St Peters about 10 am/picks up about 4 pm...£30
Free to go into St Peters but pay to go into Vatican Museums.
I have pre booked tickets for entry into Vatican Museums in July,,cost £40 for 2 people.
If you are on East Med cruise you can do most stops yourself.
P.S if you do the Rome shuttle do St Peters 1st as it can take up to 2 hours in line now they have put airline security scanners + security search to get in.if you go at say 2 pm you may not get in before coach leaves.
Johnny C