In the episode 'Pizza Face', Michelangelo briefly sings the chorus of the 'Ninja Rap' by Vanilla Ice, which is part of the soundtrack of Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991).
Pizza Face is based on an obscure TMNT villain from the 1990s - he was originally Shredder's chef, then he mixed mutagen into a pizza in an oven and was transformed into a deranged mutant-cyborg being. Pizza Face has a similar origin here, except he's an independent character and has a body completely formed of pizza.
At 16:07 into the episode on the pay phone you can see the phrase "the triceratops are here" graffitied onto its side. This is a sneaky reference to the triceratons who would later become antagonists in the series.