Collider is reporting that del Toro wants Cruise, while Universal wants James McAvoy. Sure, Cruise comes with superstar baggage that McAvoy doesn't have, but McAvoy's also considerably cheaper than Tom Cruise. Personally, if Cruise's salary affects my getting to see the things on-screen that have made men go mad in Lovecraft's stories, then hello, James McAvoy!
This is, of course, strictly rumor right now. Cruise is about to start Mission: Impossible IV and McAvoy is still working on X-Men: First Class, but both actors' schedules would allow them to come aboard by the time At the Mountains of Madness starts shooting. More as it develops.