We can see a big board in the court scene in GF2, on which Mike was entitled boss,Fredo underboss and Tom consigliere. So at least in the official definition Tom is the consigliere.

According to the "The Godfather" game by Electronic Arts (which FFC despises, btw), it specifically has a scene where Michael tells the player that Tom is out as consigliere, and Al Neri is the new consigliere...for whatever that's worth.

After watching the butchered version on Spike yesterday I had an epiphany about this nagging question. Thea answer is this: Tom remained consigliere through GFII but in title only. Michael, who trusted no one would never concentrate too much power in anyone's hands. He gave Tom that song and dance about how he had kept things form him out of respect, wehich we all agree was manipulative. Still at that point I think Tom was the official consigliere. What Michael really did, however is allow the title to remain, but he divested it of much of its power.

Compare this, for example to most Secretaries of State in government. They retain the title, which carries with it the implication that he or she is the presidents top foreign policy advisor, when in fact more often than not the chief foreign policy advisor is on the white house staff.