Alright, so obviously we're not all going to agree as to what the best Vanessa album is... but here's what I think.
For me, Harmonium and Heroes & Thieves are the best... and, while Be Not Nobody has some great moments, it's not even close to the other 2 in terms of musical complexity, vocal abilities, and melodic content.
Harmonium is more like the sophomore album to Be Not Nobody (which it is, but hear me out). Think about it: same record label, slightly more mature direction, more creative control, Ron Fair still being available, etc.
And obviously, Heroes & Thieves, seeing as it is on a different record label, is going to sound a little bit different. However, I actually think that while it can get very commercial and synthesized at times, the songs themselves are wonderful. What I think could have made this better is using the same style of arrangement and mix that they used on the two previous albums: supplementing V's inspiring piano (not synthesizer, piano) accompaniment with strings and other such orchestral instruments. Honestly, that's the only thing that I think may have obstructed the presentation of these equally wonderful songs.