So, about what percentage of the subway lines outside of Manhattan would you say are elevated? I know all of the trains on Manhattan island are subway, what about Brooklyn, Queens and the Bronx?

Most lines in Brooklyn are elevated. I would say, 85-90% of the subway stops are elevated in Brooklyn

In Queens, the N/W, 7, A and J/Z trains are elevated.

The spine of trains along Queens Boulevard - the E/F/G/R - are underground.

In Brooklyn, the A and R trains run underground their entire runs. Don't the 2/3/4/5 stay underground as well? Most other trains start out underground and then go elevated once they're south or east of Prospect Park.

Yeah, the Lex lines run underground through Brooklyn. If memory serves (and it usually doesn't!), they're elevated in the Bronx.