After recently re-watching the show (and frequently touting it as GOAT in the Writers Guild Top 100 thread), here are my votes for 10 best episodes:
10. Pine Barrens (dir. Steve Buscemi) - Season 3, Episode 11
9. Toodle Fucking-Oo (dir. Lee Tamahori) - Season 2, Episode 3
8. Made in America (dir. David Chase) - Season 6, Episode 21
7. Johnny Cakes (dir. Tim Van Patten) - Season 6, Episode 8
6. Mergers and Acquisitions (dir. Dan Attias) - Season 4, Episode 8
5. Commendatori (dir. Tim Van Patten) - Season 2, Episode 4
4. For All Debts Public and Private (dir. Allen Coulter) Season 4, Episode 1
3. The Happy Wanderer (dir. John Patterson) - Season 2, Episode 6
2. Cold Cuts (dir. Mike Figgis) - Season 5, Episode 10
1. Christopher (dir. Tim Van Patten) Season 3, Episode 4