I would have picked Turtles Forever, but since that is not an option, I will go with Wedding Bells and Bytes. It's a bit cheesy, and I'm actually not a huge fan of seasons 4-7 from the 2003 series, but this episode has a nice happy ending. (April and Casey get married!)
Turtles Forever had its flaws (the portrayal of the 80s turtles; the voices of the 80s turtles, especially Leo's
), but was still a great send-off to the 2003 turtles.
Not a fan of Carmageddon as the Nick TMNT finale.
I would prefer Owari (the final episode before the series switched over to Tales of the TMNT) or End Times (that one technically ends the main story line). Both were bittersweet, but actually made sense in the context of the series and were very well done.