Sox is the most straightforward tool for converting raw 8-bit or 8SVX IFF format Amiga samples to 16-bitt/44.1kHz WAV files. Keep in mind that you might need to play around with the upsampling parameters to get the correct target pitch.
For example, drums were often sampled at higher rates (D# or F instead of C in the highest octave of whatever tracker was used) to make them sound a bit less dull. Chromatic sounds are often at C (but not always) which means they’re 16726 or 8363 Hz depending on how far up or down whoever sampled them wanted to play them (or how much memory they had available ;)).
Amiga didn’t need file extensions to recognise file types, so you can’t know whether a file is in raw or 8SVX IFF format without looking into it. A lot of people assume all Amiga samples are raw which is why you often hear a sharp blip at the beginning of converted Amiga samples; that’s actually the 8SVX IFF header and not sample data that should have been converted.
This is all to say that automatic batch conversion might not give you the results you’re looking for; for best results you’ll need to do this manually, or in groups of similar samples and then check the result.