What adequate tools are available for estimating entropy? This question seems to touch on the apparent fact that NIST SP 800-90B is not suitable for estimating entropy produced by sources that are not uniform, despite being IID or non-IID.  It also seems that most phenomena for producing entropy are not uniform.  If that's indeed right, then naturally one wonders what adequate tools are available for estimating entropy?
Clarification.  The question is asking for tools like NIST SP 800-90B.  What programs are out there that are ready to use, hopefully with a publication to introduce it?  It seems only NIST SP 800-90B is available.
I'm assuming that you're referring to physical entropy sources, rather than Shakespeare and such.
You can go the compressive approach using strong archivers as discussed elsewhere. However, that will always leave you with a feeling of whether it's accurate enough? And this is an uncommon approach though it works for me.
The standard way, is to simply calculate $H_{\infty}$ based on the most probable value in your data set. Autocorrelation? Remove it. So ironically, your tool is a pseudo random number generator. And ent.
There is the concept of $(\epsilon, \tau)$ entropy per unit time, where $\epsilon$ is the sampling resolution and $\tau$ is the temporal sample lag.  And it goes like this:-

Sample source at $(\epsilon, \tau^{-1})$ per second. Eg. 4 bits @ 10 kSaS.
Perform IID test on sample using permutation testing.
If sample = IID, run ent -c and get ${Pr_{max}}$.
$H_{\infty} = -log_2(Pr_{max})$. Done.
If sample $\ne$ IID, reduce $\epsilon$ or increase $\tau$. Eg. 3 bits @ 5 kSaS.
Goto 1.

Permutation testing is what's done by NIST's 90B ea_iid. Or roll your own. Or use mine. That link has a lot of NIST detail. The reason the bounds are tighter is that you set them yourself as to what constitutes IIDness.  NIST uses p=0.01 and my slow test uses p=0.1 rather than relying on the perceived strength of your compressor.