I would choose any program that can handle editing at a pixel by pixel level that has layers.
photoshop and gimp are some pretty common.
also if you don't want to pay a great deal you could always get Photoshop Elements. there really isn't anything you can't do in terms of pixel art in elements that you couldn't also do in the full up version.
As someone who did a lot of pixel art in her time, I found that I enjoyed being able to work in MSPaint, but I favored photoshop for the sake of layering. It was nice that, if I messed up bad enough, I wouldn't have to redo EVERYTHING, but rather just remove that layer and work it over again. Just stuck with a nice little pencil tool, 1pt.
You can use Gimp, but if you want to learn pixel art you need to learn how to manipulate every pixel because that is what pixel art is all about. The best program for that is MS paint.
With other programs you will get over spray or a lot of pixel blending so it is harder to control the exact color of each pixel.
I use Photoshop to do pixel work, but I only use it because I like to work with a small view windows showing me what it looks like and what pixels need changed to make it look sharper or better.
If Windows paint has the little window showing you a small image, that could be actual size even if it is just the brush moving over the art that is what helps the most.
I have a Icon maker that does the same thing and I can work with small images with that because it has a small window showing you what it normally looks like. So anything that can do that helps with pixel art.
I based that on the only thing you can do in a program. Because MS Paint can't do anything else, forcing people to manipulate each pixel.
I use Photoshop and the pencil tool in there does the same exact thing, but I can cheat by selecting one pixel and use the brush to change that one pixel, and stop the color change when I feel it look right.Or I can start with a quick drawing and shape each pixel using my original drawing, but just use pixels to sharpen everything. There has been times when drawing pixel art I needed a program that only has the pixels to work with.So that is why I say MS Paint is the best, but also because it is already on the computer unless you have a Mac.