I searched Google for "peter pan anime", and found The Adventures of Peter Pan, an anime series from 1989 - close enough to the '90s.
Episode 30, entitled "The Levitation Begins! Hook's Flying Pirate Ship" (emphasis mine), has this summary on Wikipedia:
The boat seems to have driven off in the middle of the night. Peter and his band are stuck now on an island. The can't escape, because a huge fire-spitting monster fish burns everything that crosses the sea between the island and the shore. When it seems they're able to escape, a very powerful, flying new pirate ship appears, with Captain Hook on the deck ordering his pirates to load the cannon.
I couldn't find any reference to the crocodile itself being mechanical, but of course it makes a ticking noise due to the alarm clock - could that be what you were thinking of?