I like the bass tone on Images And Words best. The Spector sounds really agressive and fits the overall sound very well. FII also has a terrific bass tone, and so does TOT (I agree with ReaPsTA on that).
I also have to say that it's a shame that JM uses so much distortion these days. His Bongo could really provide a good bottom end to the sound, but much of it is taken away by this ridiculous amount of distortion (which seems even worse live, see Peruvian Skies).