There really aren't any bad dive operators in the upper keys, each is unique and has certain benefits or caters to various divers tastes a bit differently, but none are truly bad.
I gather from your question that you are looking for a 6 pack, if that is the case, then Quiesence would be a good choice. If it is just you and your two sons on the boat, you can pretty much pick the dive site you'd like to see. Most other operators have schedules posted on their websites. There are some sites that are hit regularly by a lot of the dive boats and some that don't get hit as often.
I tend to dive with Conch Republic Divers the most regularly when I'm in the upper Keys. I like the staff and the their big boat which is a Newton: it is stable when conditions are bumpy. Conch is in Isalamorada, just a bit southwest of Key Largo, and visits some sites other operators don't hit very often.
As suggested by others, Rainbow Reef is nice if you are looking for a guide. Their young staff enrolled in the instructor program are a nice group of people. They also have bigger boats that are stable when marine conditions are bumpy