The influence of the isospin-independent, isospin- and momentum-dependent equation of state (EoS), as well as the Coulomb interaction on the pion production in intermediate energy heavy ion collisions (HICs) is studied for both isospin-symmetric and neutron-rich systems. The Coulomb interaction plays an important role in the reaction dynamics, and strongly influences the rapidity and transverse momentum distributions of charged pions. It even leads to the pi- pi+ ratio deviating slightly from unity for isospin-symmetric systems. The Coulomb interaction between mesons and baryons is also crucial for reproducing the proper pion flow since it changes the behavior of the directed and the elliptic flow components of pions visibly. The EoS can be better investigated in neutron-rich system if multiple probes are measured simultaneously. For example, the rapidity and the transverse momentum distributions of the charged pions, the pi- pi+ ratio, the various pion flow components, as well as the difference of pi+-pi- flows. A new sensitive observable is proposed to probe the symmetry potential energy at high densities, namely the transverse momentum distribution of the elliptic flow difference [Delta v_2^pi+ - pi-(p_t rm c.m.].