I don't think he was, Sugar ray robinson, Sugar Ray leonard and many others were better than Ali, he just had the "superstar effect"
Leonard? Ha, no. I don't have him in my top 3 for accomplishments, but I don't think any fighter beats him at his best. I have Robinson, Armstrong, Greb, Pep and Duran ahead of him (I know I haven't seen Greb, but this is for accomplishments). Though I'm often tempted to put Ali higher. H2H he is right up there, because I don't think any HW (and therefore any fighter) takes him at his absolute best.
I think you are a little confused about this. Did you ask if Ali is in the top3 all-time, or if there were fighters that could beat him H2H? Those are two totally different things.