Maratis itself can't create much (it is just an editor) but the waves, whether in torque or cry or udk perhaps use displacement maps rather than normal maps (to actually affect the geometry), unless torque has a fluid simulation system built in.
Maratis doesn't have this type of functionality built in, but if you were to program that functionality yourself you could pretty much make your own game engine using Maratis as a base.
I am going to look into torque to see what it can do.
Edit: I just checked out torque and I see it is free. The setup is a bit complicated for me. I would actually prefer Unity 3d in that case (accept for the cost to publish with Unity3D). So it seems like Torque is best for you then.
Maratis does have a very easy to understand API though. Perhaps I will take some time out to try Torque later on.