But that's Star Trek TOS you're talking about.
First of all, old SF stuff tell us more about the time they were written in than about the actual future. And with Star Trek, We're talking about about Space race and cold war here.References and stereotypes from those subjects are kind at least understandable, like Stepin Fetchit movies (heard the first time of him today) told us about the actual racism in his time.
But episode one is a piece from the late 90s. If a cartoon character is shown with some possibly racist traits, this is simply sloppiness. Laziness to invent some actual accent, unthoughtfullness of noticing it how the characterizatzon and accent match a stereotype (it probably would have been noted if the role was casted with an actual black actor instead of blue-greyish a computer animation) and general cluelessnes of pushing that lazy, clumsy nuisance into the viewers field of vision at all.
OK, now back to Star Trek and why it can't be compared: The stereotypes in ST aren't (usually...) not Stereotypes used as a lazy way to make easy characterizations (see: James Bond: blonde guy with german accent --> evil, eyepatch: evil or a fake italian accent to depict some guy as 'funny') They're rather allegorys. Yes, Romulans are space russians, but if you want to tell about an utopia about all space races living happily federated together, you need someone to symbolize the warmongering people that has to be coped with, too.
And please note while the Romulans symbolize Cold war russia, it was poor Chekov who had all the stereotypical russian stuff!
And while Star Wars did their happy Science Fiction Fairy Tale, ST actually went onto the subject of racism (Let that be your last battlefield) - in al allegorical way with all stereotypical dead weight removed. So if someone in ST is symbolizing someone back here on earth, it can be done that it is on purpose.
And still my final point stands: If seeing a non-human character with some negative traits triggers some black/white stereotypes, it tells a lot about how deeply rooted these prejudices are within the recipient. (...maybe: too..)
But as a conclusion, I'd like to say the the whole Jar Jar character is SO annoying, and as a whole is a result of bad and uninspired writing, that perceived racist stereotype don't make the top ten on my list of reasons to wish him some unpleasant veneral diseases.