Rain Dogs is of course the closest to his “objectively best” album, and any publication that isn’t just trying to be controversial would always rank it as such. It happens to be my personal favorite as well.
Trying to think of it in external and detached terms (rather than what else might be merely “my favorite”), the next few greatest ones would be:
Those can reasonably be rearranged in any order. That just happens to be how I would rank them at the moment. I can’t abide by the idea that Alice or Blood Money are among his best works, however. They simply veer far too far into kitsch, and it’s often not even the charming kind of kitsch. Obviously this has nothing to do with being among someone’s favorite Tom Waits albums.
His earlier jazzier stuff gets a low rank from me. Half of the content is wonderful. The other half is often lower than mediocre. There’s a reason he left behind the stylings of that “other half” once he learned some new tricks around the time of Swordfishtrombones. I’d still place Blue Valentines above either Alice or Blood Money though.