Chicago kept a pretty powerful patronage-based political machine decades after most other American cities, and IIRC has the most convictions of public officials for corruption over the last several decades (though DC has it beat per capita, easy). The reputation is probably a bit overblown at this point, but there is history.
That said, of course the "Chicago thugs" label being applied to Obama & co. is just a way for folks that hate him to vent, rather than anything remotely rational. At this point, he's an amalgam of Boss Tweed, Neville Chamberlain, Yasser Arafat, Leon Trotsky, Frantz Fanon, and Ice Cube circa NWA. At this point I've given up expecting the rage to be even internally coherent.