I don't see the flags you should check when saving a VTF. Should include those in case they're not in this guide. I might just be dumb and have read over them though :)
I'd also like to add that there is a VTF plug-in for both paint.net and gimp.
I used to use gimp for making VTFs but after installing the plug-in I switched to paint.net.
Haven't tested it on gimp but I'm assuming it works the same way.
It allows you to make VTF files without the need for VTFedit and you can open VTF files directly into paint/gimp
If you save something as a VTF a window pops up: http://puu.sh/ss3z9/2952eedf25.png
I always made the template Generic (Default). Leaving it empty made it very blurry if I recall correctly.
Then go to Flags and make sure these are checked: http://puu.sh/ss3Ee/af6ea5eab2.png
I always check Point Sample as well if the crosshair only has straight lines. Point sample is the first flag in the list. It prevents them from looking a tiny bit blurry (best way to test this is by making the crosshair scale very big and compare between the 2 flags).
I don't use point sample for crosshairs with curves (like wings) because it makes them slightly less pixelated on low resolutions and I prefer playing TF2 with 640x480 because I'm a disgusting individual. It's mostly preference with Point Sample but that's how I decide.
Point Sample (optional, good for crosshairs without curves)
No Mipmap
No Level Of Detail
No Minimum Mipmap
Eight Bit Alpha (Format Specific)
credit to dolphin rider for the flags
There's no best way to make VTF crosshairs though so use VTFedit if you don't feel like installing the plug-in. In the end if all flags are checked correctly you should have the same end product with VTFedit or the plug-in