Either location is great but look at the cost difference to waterproofing the window AND compare it to the cost of turning the toilet to the left. Also do not leave a space to the right of the vanity. Tuck it right to the window wall. Hopefully the window is high enough to do this. I feel you will find putting the money into waterproofing the window will be less if this is a second floor bathroom and there is a finished room below the toilet as that opens up more renovation than you may want.

You’ve got a great opportunity here to rethink how your bathroom functions before focusing on finishes. Start by clarifying what matters most, storage, openness, or comfort. If you’re expanding or rearranging fixtures, maintain a logical flow: toilet away from direct view, vanity centered near natural light, and shower or tub framed as the focal feature. Always plan for minimum clearances (about 30" in front of fixtures, 24" between vanity and wall) to keep things feeling open. For small bathrooms, consider a wall-mounted vanity and large-format tiles to visually expand the space. Layer lighting with dimmable ceiling lights and focused task lighting near mirrors.

It is commonly overlooked that you CANNOT waterproof a window that is within the shower surround and direct line of water. Sure, you can waterproof the wall jambs/sill/head, but not the window unit itself. A typical operable window is designed to discharge water hitting it from the outside (rain), not inside. So extrusions/profiles can hold water that gets into the sash/jambs/sill of the window unit, and work it's way down inside the wall or just rot the window.

Alternatives with keeping a window are to put a shower curtain in front of window, hinged glass, or change the unit to a fixed storefront or glass block type.

The other feature that is commonly overlooked is understanding opaqueness. You will always read "just put a film on the window." However, any opaqueness less than 100% allows a shadow to be seen, and the closer you are to the window the clearer the shadow becomes. For many people, just having strangers know when you shower, or seeing a very defined silhouette, is a deal breaker.

Why a pony wall at all, the toilet is behind the door anyway.

@Lorraine Leroux shows the best layout.

If turning the toilet is not a good option, then I would just remove the pony wall and keep the toilet as-is. The shower across from the toilet would not bother me. Just make the shower wall across from the toilet something other than glass.

I prefer Option 2 - it gives by far the most light to the vanity (and least risk of water damage).

Do you have to have 2 sinks? I know you have an extra storage cabinet, but counter space is nice too - especially if this is a guest bathroom.