How much do you think you're trying to quantify, and how different are the values each method reports?

Nanodrop is cheap and 'good enough' for fairly high yield samples (20-50ng.ul-1 is about the lowest nanodrop approaches can quantify reliably, but above ~100ng.ul-1 you can be pretty confident in the values). It will not however distinguish different nucleic acids, so any DNA present will also contribute (including things like primers etc). It also doesn't care about your RNA quality, so highly degraded RNA will still absorb nicely at 260.

Qubit is usually reserved for quantification of much lower yield samples (like miRs isolated from serum etc), and is readily capable of quantifying low, low quantities: the use of dyes also renders it capable of distinguishing RNA from DNA, and potentially even making rough assessments of RNA quality.

Bioanalyser approaches aren't really intended to be used for quantification: you should generally have established whether you have RNA or not, and how much (approx) before you even start, since bioanalyser chips are fairly expensive. You would use this method to determine RNA quality/integrity, since that's what it actually measures. Concentration is something of a secondary concern, and is more or less interpolated from the migration trace post-hoc.

So, use nanodrop for cheap, cheerful quantification where you know you have large yields, and will be using fairly large amounts of RNA downstream. Here if the values are too low for accurate quantification it doesn't matter, because you won't be using that RNA anyway (you won't have enough of it).

Use qubit for very low yield samples you'll be using in applications compatible with such low yields (i.e. if you only have 0.2ng.ul-1 but have a kit that can use such low amounts, you're good to go).

Use bioanalyser for samples you've quantified via one of the above methods, and now wish to submit for some expensive RIN-sensitive method like RNAseq.

Thanks John for the detailed answer. The Qubit, however, comes with both high sensitivity broad range option. Irrespective of the sensitivity, what I am trying to work out is the most reliable method with no consideration for the cost involved.

Of the three, probably qubit, then.

However, I do think you could benefit from a bit more thinking about biological context and innate variability.

For example, I use nanodrop for essentially everything, since mostly my yields are 200-2000ng.ul-1, and all the applications I intend to use the RNA for won't really work effectively if it's below ~50ng.ul-1. If I get RNA yields so low that I can't trust the spec reading, the answer isn't greater accuracy, it's "make more RNA".

If it turns out the nanodrop is only 90% accurate overall anyway, well, that's fine: I use reference genes and internal standards to normalise for that, plus all other sources of variation. For me, more accurate approaches would be entirely superfluous, and I'll stick with what's cheap and robust.

So I would advise you to think slightly more about what you _need_ rather than just "accuracy at whatever cost".