Aww, I knew Andrew would beat me to it. Return to NY always comes to mind as top of the tops. Didn't expect oldmanwinters to highlight my other fave "Leatherhead Too" though!
It's Berger's masterpiece. Since those were already mentioned I'll also give a shoutout to Tales #55: "A Day In the Life", an introspective issue that focuses on the turtles & Splinter as a family in the days leading up to their first showdown with Shredder in issue #1, a kind of similar vibe to another fave (already mentioned twice!): #11. Those interpersonal, reflective stories are always a treat, and sorely needed in comicdom in general.