Greg and I were toying with the idea ourselves, actually.
What I was thinking is this: I'd keep my Nautilus stock. It works well and I don't want to mess with it. I'd then building an appropriate target, say the Abraham Lincoln, complete with ballast system (that's the key!) AND pyrotechnics (smoke and flare, etc...
I'd start the run with the Nautilus surfaced, running for the ship at full throttle. Blow the tanks and let her submerge slowly until the "eyes" are just visible. At about six feet out... full dive on the planes. This is realistic, as the Nautilus should be taking the bottom out of the boat, not smashing directly into her sides.
What needs to happen is that the Nautilus will clear the ship's keel without hitting her. Just when she's underneath, blow the Lincoln's ballast tanks, set off the smoke and flares, and watch her sink. You could even add a spring-loaded paddle underneath her to 'flip' at the moment of impact to get the shock.
Unless you film the entire sequence in slow-mo, I think actually ramming the Lincoln would look fakey and non-scale, and you'd still need the pyrotechnics for the full effect.
Maybe when I get more time (like.... fifty years from now), I'll do up a 1:32 Abraham Lincoln model and recreate the scene.
Anybody with a better schedule be interested in doing up the Lincoln? We could hook up and play out the entire sequence on film!