Tom was most definitely consigliere to both Vito & Sonny (after Vito was shot). It was a permanent appointment to the position, more fully explained in the novel. While never addressed explicitly, Tom was effectively minimized by Vito after Sonny was kid. As the novel stated, even Tom knew he was no wartime consiglieri as having been lulled to sleep by Barzini and the other Corleone enemies when Santino was killed. In the novel, Tom knows that Genco would have never been outsmarted by the enemy to let Sonny be killed.

Vito did not have the heart to formally replace Tom, so he let Michael do it. By the same token, Vito could not personally have Carlo killed, so he again let the burden to Michael.