Considering that Mark Ruffalo was nominated as the best actor in a supporting role for his portrayal of Mike Rezendes, who wrote the whole story for The Boston Globe, who was the main lead in the movie Spotlight?
There is none.
Spotlight is what is known as an "ensemble cast".
Individual actors in the film were nominated for several different awards, the only one that I can find for "Best Actor/Actress" was the New York Critics Award, which went to Michael Keaton. All of the other nominations were for "Supporting Actor/Actress" and all of these went to either Ruffalo, Keaton or McAdams.
While Andrew is correct that Mark Ruffalo gets top billing, that doesn't make him the star. Billing order is decided in negotiations between the production company and the actor's agents. It often results in some odd people getting top billing. See TV Tropes' articles on "Billing Displacement" and "Billed Above the Title". I am not saying that this is what happened with Spotlight, though.
Other explanations for billing order include the ever popular "he'll take a pay cut if you give him top billing" and "he'll only do the film if you give him top billing". The amusing thing is that this generally reflects more on the agents than on the actors... an actor may be very happy to do a role, regardless of the billing but, in order to get their talent up the notoriety rungs, agents will be... obstinate because they "just want what's best for their clients".
Mark Ruffalo was given top billing. Whether he is the "main lead" depends on your definition of "main lead".
The reason for the discrepancy you're seeing in his Best Actor in a Supporting Role Oscar nomination is due to the way the Oscars work. From their official rules (Section 6):
So the Academy members deemed his best suited for the Supporting Role Oscar, probably due to the fact he fairly equally shared screen time with Michael Keaton, Rachel McAdams and Brian d'Arcy James.
However, in all promotional material for the film, like the posters for the film below, Ruffalo got top billing: