Personally, having owned a lot of neck-thru and bolt-on guitars, I don't think there is an appreciable (or useful) sustain benefit to neck-thru over a well-made bolt-on. Sure, upper-fret access can be better, but a contoured-heel bolt-on is just fine for me too...
Tone does vary, I think though, like the last poster said, but I don't think either can be said to be better :)