The source linked by Wikipedia ist not very sound in this case. It is a website with the sensationalist title "Hydroelectric power's dirty secret revealed" and in its text the magazine mentions a "a study to be published" without title where it supposedly gets its information from.

You are correct, that in Brazil the biomass may contribute more, in this study from 2002 one of the highest emitting reservoirs is examined. Including everything up to the Ants colonies destroyed by the reservoir. However they note that Emissions decrease significantly after a few years as the biomass is decomposed. Also at the time of the article linked above the plant was still installing turbines, increasing its energy output. This obviously leads to wrong estimations when current carbon emissions to current power output is extrapolated over the lifetime. In 2002 a Cambridge article noted that emissions are on par with fossil fuels (which of course is still not great!) A study in 2016 noted that previous estimates of the emissions may have been quite a bit to high as they collected samples during seasons with high activity.

In summary: We don't know for certain yet how high the emissions are, but 3.5 times fossil fuel emissions seems to be grossly overestimated.