Depends on what is the factor for "best". Is it animation ? OST ? The stakes behind the fight ? The symbolism behind it ?

UBW for me, with Lancer vs Archer, Shirou vs Archer and finally Shirou vs Gilgamesh.

But HF comes very close with Rin vs Sakura and Shirou vs Kirei (as a downside, it doesn't have Kojirou vs Saber as do the other 2, and I love that fight too).

Fate route has also some great ones of course, but I prefer the fights in the others, be it for visuals, plot, emotions, themes or whatever (depends on each fight).

It comes down to UBW and HF

Sparks Liner High and Shirou vs Kirei (vn) are my favorite fights so I'll go with hf

To Hell With Unlimited Blade Works!!! The Fate Route is Better!