Lyon's comments come after Thomas' best on ground performance in Sunday's win over West Coast and five days before the Magpies take on Lyon's Saints.
"I was watching the Collingwood-West Coast game yesterday and asked Rob Harvey, 'Is he the best player in the competition?'" Lyon said on SEN on Monday morning.
"The way he chases, the way he runs from back pocket to forward line, he is just really inspirational to watch and his finals series last year was brilliant."
Many football experts had put Saint Brendon Goddard on a pedestal as the game's best player after his impressive 2010 finals series but Lyon said by the same criteria, Thomas had fair claim to the honour.
"He's been outstanding and everyone goes back to Goddard's finals," Lyon said.
"But what Thomas did in the finals and Grand Finals, I just think he is [the best]."
Goddard has been underwhelming for much of 2011 so far but Thomas has gone from strength to strength as one of Collingwood's most important players.
"I was there against Adelaide and [Thomas] really turned that team around with his fanatical chasing," Lyon said.
"He covers that much territory. He's almost the best player in the competition. He's unbelievable. I really admire him.
"Not only what he can do with the ball, like his left foot snap [and goal in the second quarter], but he'll run from the forward pocket to the back pocket to spoil the ball and get in the way."
Goddard is likely to take his place against the Magpies on Saturday after he was rushed to hospital with what looked to be a serious neck injury in the first quarter of Saturday's win over Fremantle.
Sean Dempster was also hospitalised after he was knocked unconscious in the dying minutes of the win but Lyon said he was confident both would be declared fit for Saturday's games.
"I'm pretty confident Goddard and Dempster will play, depending on the finer motor skills and the testing but they flew back with us, they're in pretty good shape."
