There is a good wikipedia article on this subject, which has a lot of
references that seem to be of high quality. You can also go to
amphibiaweb.org or the national biological information
infrastructure.
The "killer fungus" is not the only cause these sources mention. Other causes
include habitat modification and fragmentation, pollution and climatic
change.
It's certainly possible to count numbers of amphibians and it is not
necessary to count them all to know that there is a dramatic decline in
their numbers. If a sufficiently large number of populations around the
world is counted accurately over a long enough period, and those
populations are seen to decrease in numbers all over the world, I would say
it is safe to speak of a global decline in amphibian populations.
Concerning the causes and what we can know about them: we can study the
data, e.g. look at whether there are differences in decline rates between
different types of populations (cool or warm climate, human density, food
sources, amount of pollution), and we can study the effects something like
the fungus has on individual amphibians, or on populations.
It's fairly easy to find a lot of information on this topic, from pretty
reliable sources. I don't think skepticism is warranted here.