In the books it is mentioned several times that dragons do not grow as large when they are kept in captivity. Mike gives a good example of this in his answer. Also:
Drogon is the largest of the three living dragons. Although I believe he was always the largest dragon, it is worth noting that in Meereen he was roaming free instead of being locked up under one of the pyramids.
As to their extinction, Marwyn hints in AFFC that:
The Citadel was behind the death of the last dragons and that they have been actively trying to build a world bereft of magic
All that said, it is still not explained whether:
The disappearance of magic caused the dragons to die, or if it was the other way around.