Sonny saved Tom from the streets. Sonny and Tom grew up together and were roughly the same age. There was a deep reservoir of shared experiences that Tom didn't have with Michael. So Tom feels free to speak his mind and occasionally show exasperation or lose his temper with Sonny.

Michael is just colder and quieter than Sonny. Tom doesn't have a brotherly relationship that he had with Sonny nor does he have the father-son relationship he had with Vito.

When Michael takes over, basically Tom is just like any other mope in the corporate world where there's been a change of management. He's just out of favor. Nothing personal, just business.. \:D

"When the snows fall and the white winds blow, the lone wolf dies but the pack survives."
Winter is Coming

Now this is the Law of the Jungle—as old and as true as the sky; And the wolf that shall keep it may prosper, but the wolf that shall break it must die.
As the creeper that girdles the tree-trunk, the Law runneth forward and back; For the strength of the Pack is the Wolf, and the strength of the Wolf is the Pack.