My novel has two main characters--but my query only has one. It wasn't easy to get there. I went through a LOT of revisions until I managed to cut the second MC out. The result leaves out a LOT of the plot, but it still works.
I think the key to remember is that the query isn't really a mini-synopsis at all. It's fishing.
You write a good hook to snag an agent's attention.
You lure them in with unique bait and curious movements.
In conclusion, you reel them in with a solid plot-line and a strong voice.
You only NEED one MC to catch an agent's attention. Once they take the bait, they can be surprised by what you've cooked up. Agents KNOW it's impossible to condense an entire book in a couple of paragraphs. That's not what they're looking for in a query--that's for the synopsis and full requests. A query is only intended to tell them that you've got potential and you're worth the time it takes to read a partial or a full.
For my query--written for a novel which follows both MCs from third-person limited during separate chapters, then weaves the two POVs together--I wrote as if only one MC existed. Was it easy? No. Over half the story is about a completely different character. However, each character has their own story. Be more decisive and just pick one. Once you decide who you're going to write your query about, remember that the query is focusing on their role, their perspective in the novel--not the overall plotline. Cut out his interaction with other MCs and focus on what he/she gains from the interaction.
Gah. I'm probably making this confusing, so here's an example:
Alice and the Mad Hatter goes to a Tea Party, but the White Rabbit's sudden insanity turns it into a party celebrating the Red Queen's dark revival. The Mad Hatter must search for the White Rabbit's lost pocket-watch to return him to normal while Alice distracts the Red Queen with the help of a dozen Spades and two Clubs. Only with perfect timing can the Mad Hatter and Alice stop the revival--assuming they don't die first.
That's too many characters. It becomes a jumble that is difficult to read.
Edited to focus on Alice:
Alice goes to a Tea Party, but the Red Queen's dark revival leaves her seeing red. After being isolated from her friends, her only choice is to distract the Red Queen from her bloodlust with frivolous games. Unfortunately, Alice realizes a little too late that the Red Queen has become harder to amuse. Alice might just lose her head if she loses the game--assuming the game itself doesn't kill her first.
Pardon the quality since I wrote it on the fly, but I hope that helps you understand what I'm trying to say. The second version doesn't mention the Mad Hatter or the White Rabbit at all, even though the conclusion to Alice's story relies on him.