So, a flying boat? Sometimes the simple approach is best. Take a flight base of your choice and attach it to an actual gondola like this one from TTC's Carnevale range:

The underside will be flat, but adding a bit of detail shouldn't be hard and it won't show on the table anyway unless you have very, very tall flight posts or very, very short players - or some weirdo does mirrored bases like an old-timey pervert trying for upskirt peeps on his dance partner using mirror-toed shoes.
Adding some landing gear (maybe like helicopter skids?) would emphasize the flying fantasy boat aspect, while leaving it flat bottomed and having a removable base would let you use it as a regular gondola, which is handy for Ghost Archipelago and the like.
The Evil Empire used to make an elf eagle-drawn flying boat/chariot thing called a Lothern Skycutter, but it went OOP a while back. You probably don't want the eagles anyway, and I do see several listings for fuselage bits online, so maybe some potential there too.
Me, I'd go with a regular gondola though.