I recently came across a paper where the authors protonated their molecule in ACN using HBF4.Et2O. My question is, if I had a solvent mixture of 90:10 MeOH:H2O, would the HBF4.Et2O acid work better compared to HCl? Is it a superacid?
Yes, it's a stronger acid than HCl, and the authors of the paper you mention probably wanted to work in anhydrous conditions, which is why they chose HBF4.Et2O.
I suppose technically it's measured pKa (in DCE) is lower (more negative) than H2SO4, which would make it a superacid. But if i'm not mistaken the HBF4-Et2O complex will react/decompose in water and liberate Et2O and form H3O+BF4-.
If you are stuck using a MeOH/H2O mixture, you are going to be mostly limited to the acidity of hydronium with some minor solvent effects for the presence of MeOH.
Article Acidity constants in methanol/water mixtures of polycarboxyl...
Given that, it may be more useful for you to try H2SO4 unless you can use anhydrous conditions.
If you are particularly interested in the BF4 counterion under aqueous conditions try going with a solution of prepared HBF4 in water https://www.sigmaaldrich.com/catalog/product/sigald/207934?lang=en®ion=US
It's also generally cheaper and easier to handle.
Interesting somewhat older paper that may prove useful: Article Equilibrium Acidities of Superacids
in water everything is leveled to the acid strength of H3O+. The only reason to use different strong acids is if the counterion makes a difference. So if there is a particular reason (solubility, ion pairing etc) to want BF4- as the counterion.... then you want to use it.
so it is sometimes used in diazonium ion modulated syntheses because the BF4 salts are insoluble and precipitate, and when heated are then fluorinated, F replacing N2 of the diazonium.
but if you just need a proton it isn’t any better than any other strong acid.