Having binged watched the first and second season recently, here's a few good ones.
From "Slash and Destroy"
After Donatello nearly blew up the lair and Raphael's pet Turtle Spike in the process, Raph decides enough is enough and takes the last vile of Mutagen from Donnie's lab for safe keeping until the "Mad professor gets his act together."
Raph is called over by Mikey to help out with the cleaning of the lab and he still is very cross with the situation. Luckily, Master Splinter has a sure way to calm Raph down again.
Splinter: Raphael, allow me to make a suggestion.
Raphael: Suggest WHAT Sensei? I'm tired of suggestions, what could you possibly suggest...
(Splinter touches a pressure point on Raph's collar bone which paralyzes him and makes him fall over backwards.)
Splinter: Perhaps you should sit down and meditate for a while.
Donnie gets all busted up during his encounter with Slash But however severe that beating was, it sure didn't beat the sarcasm out of him.
Donatello: Ugh… What hit me? It was like Raph, only… bigger and meaner… angrier, but… not quite as ugly.
Raphael: It was Spike! He got into the mutagen--
Donatello: Spike?
(Rolls his eyes and continues in a sarcastic tone)
Donatello: Way to keep that mutagen safe, Raph.
During the Turtles' fight against Slash, Leo has been occupied with trying to get that rogue canister of Mutagen which thanks to a streak of Bad Luck seemingly always gets away from him. The apotheosis coming with a simply hilarious scene in which he had tea time with a little Girl who in the Nick Comics is named Chloe, who tries her hardest to teach Leo proper etiquette.
Chloe: No, no, no, no, no. You have to hold your pinky out.
(Leo looks at his hand, which no matter how you slice it, has only three fingers.)
Leonardo: I don't exactly have a pinky.
Chloe: Are there other talking turtles like you?
Leonardo: Nope. Just me. Mr. Imaginary turtle.
(Raph and Slash fall through roof)
Leonardo: Raph?!
Raphael: Leo!? Having… tea time?!