I love George Thomas! Here's a great Smithsonian article on him and his career.
http://www.smithsonianmag.com/histo...84/?no-ist=&=&onsite_campaign=SmithMag&page=4
I think he was an excellent commander, with Nashville perhaps being the best example: he destroyed an entire army. He was also an excellent subordinate to Rosecrans- through Chickamauga, Chattanooga and other engagements. I also think he was certainly very underrated- because of the personality conflict he had with Grant, who along with Sherman and some others did seem to want to diminish his accomplishments. Also, the hyper focus on Confederate generals and a certain narrative that prevailed after the war edged him out of Southern writings as well.
The biggest accusation that has been levelled against him, is that he was "slow"- a criticism made by Grant and others, which I think stemmed from a different command style than Grant- Grant wanted, as I think diane has noted, things done
now, something that Sherman was only too happy to comply with. Thomas was methodical and not about risk his men's lives if he could help it.
It's hard to say that he was the best Union commander, though, simply because we don't know how we would have done commanding all the armies- we can't compare necessarily compare him to Grant or even Sherman, because we simply don't know how he would have done in their shoes. I'm going to still go with Grant, who by the ordain of fate got to wield a lot more responsibility and ultimately did more than him for the Union victory, and put Thomas at number two (tied with Sherman for today).