Yeah, Stinkfist and Lateralus are amazing. Lateralus would be my #1 too, and Stinkfist isn't too far away.
I'd place 'The Grudge' definately higher though. It perfectly captures Lateralus' album atmosphere AND it kicks a lot of ass. That scream by Maynard is one of my favorite screams in rock music, especially how he fires it off. The outro is one of my favorite Tool outros as well. That's my only complaint with Tool: They don't rip it up enough on some albums. Luckily on 10,000 Days they solved that problem, but they also lost some of their 'Tool-ness' with it. A good sacrifice, 10,000 Days is such a fun album to listen to.