As a quick guide to sprite and tile sizes your best using binary numbers. 16x16, 32x32, 64x64 etc. You'll find that most pixel art games will use one of those.
One benefit of this is when you use tiles, just make them/the layout a binary number (512x1024 for instance) and you won't be left with any gaps at the edges.
As for window size, I just stick it to scale outer and again use some binary numbers. I also advice using equal measurements (128x128 for instance). Think of it more like zooming a camera
My go-to setup these days, at least for rapid prototyping is:
- 16x16 grid for sprites and tiles
- 128x128 for window size
- 1024x512 for layout size
Obviously, the bigger you go the more detail you require. That's why I'm a fan of 16x16 for prototyping.
As a final note, try to NOT scale your pixels. Keep everything to 1 square to 1 pixel where possible.