Hope I can offer some help!
Wayden would have shoved the small, stuttering new boy down the stairs, but the wizard in his mind advised him not to. He hadn’t even known he hosted a wizard (much less an annoying, pontificating, sanctimonious one) until recently when the three moons began to converge, an event that hadn’t transpired since his birth almost sixteen years ago. [this paragraph is a little confusing because it's in past tense, which is at odds with the rest of the query in present tense. I get that you're talking about events in the relative past, but I think it could be reframed in present tense because the switch is jarring. Another thing that's a little confusing is how it seems to go backward in time, from being confronted with the small boy, to finding out he's hosting a wizard, to his birth...I wonder if you rearrange the sequence of ideas if it might flow better. I think being a host for a wizard is the most interesting part of this, so starting off with it might be a better hook]
The small, stuttering boy in question is named Rif. He’s a Tulkarian, the same race as the sky raider who put an arrow into Wayden’s mother before flying away with Wayden’s brother Mavik tied onto the back of his winged wolf.
Wayden is determined to rescue Mavik and eventually, overcoming prejudice, enlists Rif’s help. [can you clarify why he thinks Rif might be helpful?] But Rif faces problems of his own. He too has a wizard in his mind, several of them in fact, and has been blacking out lately. One of his wizards possesses a forbidden magic known as soul stealing, an art that may lie at the heart of their mysterious soul-hosting situation.
Dead people have been turning up everywhere Rif goes and the Tulkarian is accused of being the infamous Red Killer. [having no idea who/what the Red Killer is, this falls flat to me] Wayden is determined to prove Rif’s innocence, but to do so he must confront dangerous suspects, a girl who hosts a wraith, a man who hangs out in alleys practicing soul stealing magic as a form of drug dealing, a girl who hosts the soul of a murderous immortal. [I've heard that you should avoid lists in queries] Wayden meets enemies and allies, and it’s often hard to tell who is who, especially when some of them are within his own mind. I think you could use some specificity here at the end. I feel like this last statement--not knowing whom to trust--applies to so many stories, fantasy or otherwise. What exactly does he have to do, and what does he stand to gain/lose as a result of his actions?
Mainly I think this would benefit from a little more focus. You have a lot going on here. It might be good to take a step back and isolate your character, the problem/conflict he has to solve, and what the stakes are. If you get down to the bare bones, you can then build up the detail around it in relevant places.
For example, I think the wizard mind-sharing is super cool but with the way the story is presented here, it doesn't seem to have much bearing on the plot. The way it's reading to me, the core elements are: Wayden wants to rescue his brother and enlists Rif's help [because...?]. But Rif is mistaken [how/why?] for an infamous killer. In order to continue the search for his brother, Wayden has to prove Rif's innocence by finding the real killer. If he fails, he'll never see his brother again.
Everything else feels extraneous unless it can tie into those core elements in some way.
I hope this was helpful! Good luck!