They're pretty different. I don't live very close to either, but am still connected there by friends/colleagues.
Toronto seems to have a more developed underground scene. Lots of hardcore and punk rock goes on down there, though there is more indie rock than was happening 5-10 years ago. A lot of venues apperently only rent out their space to musicians who have to then promote and sell tickets to their own shows.
Montreal has a good music scene and many venues. Lots of indie rock/pop along with experimental electronic stuff in the underground scene.
Again, I don't live in either of these cities. This is just my understanding of their respective scenes from the outside.