I dont remember seeing any places selling pizza while I was in Basel for a week or so. I dont say that there arent, it is just not that common. Maybe then I m wrong, but I remember most places having fondue, or gordon blue, some asian ones too.
The best restaurant has to be Cheval Blanc in the Hotel Le trois rois, 2 michelin stars (18 points in Gault Millau). I didnt have the chance to visit it as it was closed, but went to the other restaurant of the same hotel, (no stars but Gault Millau 13). I remember having an amazing lobster bisque. (Also remember a small bottle of water was about the same price as the lobster soup ).