Depends on what you want to do with the file. Most scanning software can scan as tiff, png, jpg and sometimes pdf. In each of these cases the resulting file is usually a raster file. The exception is software that can convert text into edible text known as OCR, or have some time of auto trace feature for converting artwork into vector objects. This is where pdf would shine compared to the other formats. Tiff is the only remaining one that can also save live editable text.
As I said once the pdf is imported into illustrator, what format you choose to save from there will depend on what you plan on doing next with it. Ai, pdf, psd or tiff would make good candidates for master files. (A file you can re-edit at a later date with no worry of degradation) And then each of these formats have their pros and cons.