Tough question. I'll pick her then: Dantalian - The Mystic Archives of Dantalian. Requires Huey before she shines though.
are we talking best girl for us readers or for the MC? if it's the MC, then the best girl goes to kiriha from 'tsugumomo'. she not only readily provides sexual services to the MC, she also brings in other females and overall takes relatively good care of the MC. (while also having fun from time to time). for the reader, it's personal preference, and i don't have one at the moment.
If I had to pick...then Holo from Spice & Wolf, Ayano from Kaze no Stigma, or Ferris from Densetsu no Yuusha no Densetsu because they have such a good rapport with their partners. Or the quintuplets of Go Toubun no Hanayome. . . . And then I remembered Absolute Choice. Too many best girls in Absolute Choice.
Best Waifu? You know there is this one saber. She sooo cute and sooo strong... As told by a certain perverted female Caster. And also there's an archer that keep saying "I'm A Man"
For me, it's Gandire Alea. The reason I nominate her is because she has a lovely personality. And a beautiful heart.