We all know the first line of a query is your "hook." I call the last line the "sinker." You want it to punch them in the face, in a nice, friendly kind of way that makes them unable to forget you after having read the 300 other queries in their inbox.
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Chicago, 2007: a skyscraper-dotted, wind-swirling dream of a city filled with aching promises and nighttime delights. For two married janitors, David and Mary, it’s a dystopia. This is a great hook. The only advice I would have would be to take away the colon and work the location / time into the sentence in a less straightforward manner.
It didn’t start that way. It never does. This second use of a choppy sentence kind of breaks up your flow. After all, I'd drop the "after all" but that's a personal preference it’s here that David, a half-black man who’d rather be full-white, meets and marries his white wife on the happiest day of his life. But it’s also where they learn that their six-year-old daughter, Penelope, will die unless they can pay for her medicine. I think it would be important to note here exactly what the illness is. As their insurance company’s manager forces Mary into twisted sexual servitude in return for saving Penelope, David learns, even to half-blacks, this city is not kind. Perhaps more of a concrete notion of how David's race plays into the plot. So far race has been mentioned twice, yet it doesn't seem to be a driving voce plot-wise.
While Mary—a devout Christian but even more devout mother—descends into a spiral of guilt because of the manager’s demands, David searches for another way. The money the manager’s promising isn’t enough. Their only other option comes from those David tried all his life to distance himself from—the poor blacks of Chicago’s south side. Not clear how going to poor people for money is an option? The ones his black (and bruised) mother had told him to stay away from long ago. Here is more implication of how race is important to the novel as a whole, but I think you still need a reference as to why David feels this in the first para - or strike the reference there. I think you could do the second one easily as it's not lending anything to the query that this second para doesn't already address.
Mary goes to them without a second thought, and David has to deal with it. It’s the only way to save Penelope; these people’s underground methods of fundraising might be able to pay for the medicine. I think this needs to be made clear in your first reference, otherwise it leaves the reader wondering. Also, I think more info about the underground methods is necessary. Now, none of David’s childhood lessons matter. To beat this city, all one has to do is survive, but for David and his family, that's the hardest part.
This is a well-written query with an excellent hook and what sounds like an emotionally charged plot. With the already addressed little nits above, I would add that you need a little bit more of an amp on that sinker. Right now it's very generic- tell us more about how David feels about going to the people he was taught to avoid for assistance in order to pack more of a punch. Give us more than David "has to deal with it." It sounds like the driving point of the book is race related, so hit on that in your closer in terms of your MC's emotional state.