  The observation in the GeV band of distant blazars has been recently used to
put constraints on the Extragalactic Background Light (EBL) and Extragalactic
Magnetic Fields (EGMF). To support such claims one has to assume that the
leptonic component of the electromagnetic cascade initiated by blazar
gamma-rays is deflected away by strong enough EGMF, suppressing the signal in
the Fermi window. Apart from magnetic fields, the development of such a cascade
might be affected by plasma instabilities due to interactions with the ionized
component of the Intergalactic Medium (IGM). In this paper we model the
electromagnetic cascade through a Monte Carlo simulation in which both effects
are taken into account separately, and we derive constraints on these scenarios
from the combined Fermi-HESS data set. In the specific case of 1ES 0229+200
observations, we show that both explanations of the GeV flux suppression are
compatible with the available data, specifically by assuming a magnetic field
of $B \gtrsim 10^{-16}\,\rm{G}$ or an IGM temperature of $T \lesssim 5 \times
10^{4}\,\rm{K}$ along the line of sight. Future observations of the spectra of
high redshift ($z\lesssim 1$) TeV objects will help to distinguish magnetic
field and plasma effects on electromagnetic cascades in the IGM.
