Looking for recommendations for a tour company to Greece. Want to do some mainland touring and an Island cruise with stops in the Greek Isles and on the Turkish coast. Looking for mid to upscale companies. Thoughts?

Go with a company based in Athens so you have a 'local' resource in case anything goes wrong. Check Fantasy Travel and Dolphin-Hellas Travel websites. They will be able to help you design the tour that best suits your travel style.

These are the two most widely recommended agencies in Athens. They have excellent reputations for communication, reliability and follow-up.

Although we never use travel agents, we did use one in Athens for our month in Greece and found it to be very helpful dealing with ferry schedules, etc.We also found that when we checked into every hotel, they mentioned the Athens based agency had sent us and we felt that using a local agency was greatly appreciated and much to our benefit.

I am not sure if you mean an "accustomised" tour through an agent or join one of the popular tours while on mainland. There are three companies running identical tours in the most popular sites on mainland (Delphi,Meteora,Mycynae,Olympia and the like), google for Key Tours, Chat TOurs,G.O. Tours...
I am not familiar with cruises, you may have to have a look on the cruisecritic site but to be honest this is definately not the best way to see the Greek islands. It is a nice way to enjoy the sailing experience and what cruise ship has to offer, but not a suitable way to explore the islands.