To answer the very title of this thread "Best Squirrel shooting caliber" - difficult. I think perhaps this changes with the person.
Some, with mostly running shots in the trees, might think a 20 bore cap or flint would be best. Those who can wait for still shots, might like a gun that performs wonderful accuracy for them to make head shots. I think in this context, the best might be the most accurate. That might be a .40, .45 or .50 or even larger - what's the most accurate.
What the ranges are, dictates calibre to some extent. The larger the bore, generally the more accurate the rifle - however, past .40 cal. the accuracy improvements might not show much at squirrel ranges.
Heavier charges in small calibres that give such flat shooting over 50yards, tend to be hard on the body shots- thus head shots are needed. The more accurate rifle, the better for that, of course.
I have a nice little flintlock .32 squirrel rifle, but if needing (rather than just out for a fun day) to fill my larger with squirrels, I'd probably take the flint .40 - or .45 - they are simply more accurate than my .32, thus, they arer better squirrel calibres - for me.
For other people, perhaps other calibres would be "Best" - for them.