I don’t recall for certain and haven’t tried this myself, but I think in CMAQv5.3 you can enable the output of marine gaseous emissions by setting the run script variable MG_EMIS_DIAG to TRUE, as documented here.
In CMAQv5.4, you should be able to accomplish this by editing the Desid_Diag section of the DESID Control File to output emissions for stream MGEM.