While it's not a query letter, the blurb on the back summarizes the story succinctly. It starts with a hook involving both story lines, then gives a paragraph to the first story, another to the second story, and brings them together with a final paragraph:

<Quote>
Two orphans on the run, each with the power to save the world ...

When streetwise Molly Templar witnesses a brutal murder at the brothel she has recently been apprenticed to, her first instinct is to run back to the poorhouse where she grew up. But there she finds her fellow orphans butchered, and it slowly dawns on her that she was the real target of the attack. For Molly carries a secret deep in her blood, a secret that marks her out for destruction by enemies of the state.

Oliver brooks has led a sheltered existence in the backwater home of his merchant uncle. But when he is framed for his only relative's murder he is forced to flee for his life, accompanied by a agent of the mysterious Court of the Air. Chased across the country, Oliver finds himself in the company of thieves, outlaws and spies, and gradually learns more about the secret that has blighted his life.

Soon Molly and Oliver will find themselves battling a grave threat to civilisation, an ancient power thought to have been quelled millennia ago. Their enemies are ruthless and myriad, but the two orphans are also aided by indomitable friends in this endlessly inventive tale full of drama, intrigue and adventure.

<End quote>

I hope that perhaps this helps,
Pat

1. First POV storyline up to convergence point

2. Meanwhile, (second POV storyline up to convergence point)

3. Merged storyline to end of story.

If your stories truly don't intersect or not until the end, this structure might not work for you.