MS Paint is fine, too. It's the pixel program, after all. I used that for my avatar. (GIMP for making it transparent and animate it, but that's irrelevant.)
I'll recommend that for starters.
You won't have to download it, either. It's already there, in your system. If you're using Windows, that is. Try searching for it if it's not on your desktop already.
As for the programs you mentioned, I think SAI is for more advanced art, and suits better for those with a working tablet. It has a binary tool, but I have no idea if it has a binary eraser. I couldn't find it with the trial version I had, at least.
Paint.NET is mostly for graphics. It does work for pixeling, though. But I'm not really sure about it, I haven't used it in ages.