I agree that you should fix it before converting to MP3. If not then most audio editing software has what you're looking for.
If you have to work with the MP3 file, there are supposedly some editors out there that can modify only certain frames in the MP3 file while leaving the others unchanged. This can help when editing only small parts of the file (very begging or end) without having to re-encode the whole file as MP3 and have more loss in quality throughout the file.
But most noise removal/click-pop removal editing needs to be done on the whole file anyway, so...
You will probably just have to use an audio editor.
Adobe Audition has noise/click-pop removal built in which is very good. You might be better off just finding a WAV editor that's free/cheap if that's all you need though.