Is there a manga where the best friend of the male mc turns out to have been a girl all along (everybody just assumed (including the mc) that she was a boy because she looks, dresses and acts like one), and then the mc and that girl end up dating?

The other way around works too ( like Onyanoko Darling )

Say hello to tomo-chan:
https://www.mangaupdates.com/series.html?id=120945

Seiyuu Ka! would fit, but it's the girl who's the main character. Also in Chang Ge Xing.

This also happens in Anata to Scandal, but it's not the main character. The main character is a girl who likes the "boy." And I think the guy knows the whole time anyway.

You might like Ashi-girl. It's time-travel/historical/comedy. The girl is the main character.

Some that are reversed are Tobenai Majo & Oiran Girl.

I know there is a manga about two male best friends and one gets sick. The other goes to visit and it turns out the reason the other got sick was because he was really a she and didn't know it. I can't think of the title right now I'll look but maybe someone else might know it for you.

Found it Kanojo ni Naru Hi