Word for a hole in the ceiling of a cave?

Solution 1:

These are commonly referred to as a skylight

eg Skylight Cave in the USA: http://ohdgrotto.caves.org/culture/photo-galleries/category/2-skylight-caves

also the Sanmenhai cave in China - from http://en.wikipedia.org/wiki/Sanmenhai "The cave is unique in that it features seven skylights that mimic the layout of the constellation Ursa Major..."

They are most commonly found in the type of cave called a "lava tube", which is a sort of tunnel left behind by flowing lava, since they tend to have a relatively thin ceiling.