In "D.W. and Dr. Whosit", the Doctor Who-like tv show Dr. Whosit features a cyber-manatee. This isn't technically a manatee appearance, since the creature more closely resembles an orange elephant.
"Wetlands" (Season 3 Episode 17) shows manatees as an example of endangered species in the wetlands.
"Marine Mammals" (Season 4 Episode 3) contains footage of manatees.
The Fuzzytown Friends' teacher, Mr. Kelly, is a recurring manatee character.
"Sam the Sea Cow" (Season 10 Episode 3) is about manatees.
In Episode 3032, the segment "Under the Sea" contains footage of a manatee.
In Episode 3069, the Creature Feature included the song "I'm a Manatee", sung by Christopher Cerf. This segment is repeated in Episode 3188.
Episode 5221 contains an animated segment called "8 Manatees".
"Swimming" (Season 1 Episode 6) shows West Indian manatees, well, swimming. :)