Any suggestions for a reliable agency doing independent tours.

Independent and tour don't seem to go together.

Do you mean a solo tour?

Are you looking for a company to book both your air/hotel, but independent travel once you reach your destination? You need to clarify that and where in Italy are you headed?

Do you mean a tour or a package. Usually tours keep moving very quickly.

If you want to got to only 3 places - presumably for several days each - you can buy a package with air, hotel and transfers - for as many days as you want - and then just do as you please.

It would help if you qualify what yuo mean:

How many days
Who/how many in the group
budget category

If you really want a tour (riding on a bus all day - there are a gazillion companies)