Torpedoes, depth charges, and nukes all work, yes.
Raven bombs can hit them, so do Gauss guns (Dagger the hovercraft raider has one).
AFAIK melee works too (on shore or if you load a melee unit onto a Surfboard).
Anything else can damage submarines if it has enough AoE and hits the surface above them, but suffers from a 95% reduction.