Probably S3.
We get Willow making her first, tentative steps towards becoming a powerful witch, she has insecurities but they don't define her like they did in Season's 1 and 2, and she's still got that cute, vulnerable quality that she loses in Season 5.
We get Willow trying to be the slayer ('Anne' 🙂), meet Willow's Mom (which explains a lot about her and gives her some great lines- 'fill me with your black, naughty evil!' 🙂) plus her sweet romance with Oz.
AH gets some great material this season - The Wish, Amends (Willow trying to seduce Oz before they decide not to have sex.), Doppelgangerland (where AH plays four characters- Willow, vamp Willow, and the two of them pretending to be each other!). Choices (bravely facing down Faith- cool, and deciding to stay in Sunnydale and help Buffy fight evil- sweet/heart felt) and her and Oz 'consumating' before Graduation Day.
The only downside is the whole Xander/Willow thing that goes on too long and is a pointless way of breaking up the two couples.
Other contenders for her best season are S4 (Willow's angsty season- she spends a lot of time crying. generally being miserable/worried. 🙁), and the end of S7 (Actually from 'Orpheus' onwards) where sweet, brave Willow seems to reappear (after being absent since S5) just in time for the end of the show. Yay.