I could be wrong, but i'm pretty sure that the Moat, Great Hall, VIA Concourse all fall under the city's responsibility; while the York and Bay Concourse would be Metrolinx responsibility. I'm not sure about who's responsible for the Union Food Market area though. The areas that smell like piss the most around Union station and where there are the most loiterers are in the moat spaces, which means city contracted security arent doing their jobs.
In any case I dont know what 311 would even do in this kind of situation, this is something that the city should be directly aware of. Heck the city has some offices in Union station so it should be even more glaringly obvious. Dont get me wrong i've got no issue contacting 311 (they've been pretty good when i've reached out to them about concerns), but I dont think it would do a lick of anything in this case. If the city cant see that there's an obvious abject failure of responsibility here, then that's a bigger concern altogether.
@DSC mentioned Scott Barrett being the manager for the city part of Union station so maybe it's time to get in touch and let him know how appallingly bad this has gotten.