Since each scanner is going to use different software that will have its own unique list of setting, I won't spend much time describing my scanners software. What I'll do is cover the basic settings common to most scanners, that will be used to get a good line art scan.

First, set the scanner to scan in "Grayscale" (my scanner calls it B/W Photo), choose a resolution (I chose 600ppi, we'll talk more about that later), if you have a descreen option choose non, if you have a filter option choose non, and choose a percentage for size. If your scanner has good software, you could make adjustments to the image (such as Levels) with the scanner software. I'll make the adjustments in Photoshop.

How do you find the correct resolution for your image? If you plan to print the line art on a desktop printer, find out the resolution of the printer and scan the image to match that resolution. For instance, if the printer prints at 600dpi (dots per inch) then scan the image at 600ppi (pixels per inch). This makes the pixels in the image the same size as the smallest dot that the printer can print, giving the highest image quality possible. It's understandable to think that, higher resolutions always give better print quality. Not so. If you have a 450dpi image and try to print it on a 300dpi printer, the printer has to distill the image's pixels so that they will fit into the printer's pixels per inch, throwing away the extra information and resulting in a lower quality print.
If the image will be printed by a commercial printer a resolution of 1,200ppi will work well. Higher resolutions don't make a noticeable difference, but does increase the file size.

After making the settings, scan the image.