I like NIN, but this really isn't even close, and I'm shocked at the results so far. Tool is almost perfect in every facet -- composition/writing, instrumental performance, lyrics, vocals. Every record besides 10kD is a masterpiece, and even that one falls just a peg or two short.
NIN had a couple great records -- TDS and Fragile -- but everything after that felt semi phoned in. Trent's vocals are mediocre to the point of detracting from the music at times, where MJK is probably the best vocalist in post-grunge rock. Trent's lyrics range from passable to cringe-worthy, where MJK's are consistently wonderful.
Trent has a much wider array of talents than any one member of Tool, and obviously a much better personality, but that shouldn't really sway anyone's vote. It's just become cool to hate on Tool unless you're a big fan... it's like no one can have a nuanced opinion on them.