Hmmm...that is a dilemma! Typically, I would say stop at the edge of your countertop. I would also typically say treat both walls the same, all the way to the ceiling. But in addition to your countertop and window frame being a few inches off, your wall runs into a door.

I'm thinking you should run it to the ceiling on this wall also and end it with the edge of your window, possibly running the tile down alongside the lower cabinet? If you don't go to the edge of the window frame, in any application, your eye will keep going to that window being a few inches over from the counter's edge.

I'm anxious to see if you get some expert advise from tile/kitchen designers...

Stop where the counter ends, not where the window ends. Its such a small space so it won't be an eye sore at all.

I agree with Royal Q&S, above, but another idea you might consider is to tile the whole wall area (at this end, too). Yes, it's obviously a lot more tile (and work), but it would carry the theme you started in the other corner, and it would take the eye away from looking at the mis-aligned windows and countertop situation

Interesting windows in front of the sink, I can understand the confusion as to where to stop your tile. What about only tiling behind your cook top only and leaving the rest as painted wall? Simple and efficient.

I agree with Royal Quartz. It won't be a big deal at all.

there are comments on your other version of this too, make sure you see them all.

https://www.houzz.com/discussions/where-to-end-the-backsplash-dsvw-vd~4086471

That looks really nice. Good choice!