Ugh. Shakes head. Why do people suddenly lose touch with reality when Bruce Lee is discussed?
I'm not an Ali fan nor a Lee fan, though I respect both men. I'll answer based on what is factually known, not based on fantasy, conjecture, or fanboy-ism.
Ali in his prime: professional fighter. All he did was fight. He spend a lot of time taking hits from a lot of guys a lot bigger and a lot stronger than Bruce ever thought about being. And Bruce thought about being pretty darned strong. When Ali wasn't fighting he was training to fight. He studied and knew every fighter he went up against. He had the finest trainers and coaches who's entire life revolved around making Ali win. Also, most boxers have their own share of undocumented 'street fights' under their belt.
Bruce in his prime: professional actor. No documented fights. Hard trainer, no question. Superb martial artist, no question. Great innovator no question. When Lee wasn't making movies he was training, innovating, and experimenting. But he wasn't training exclusively to fight and he wasn't fighting on a regular basis. He put out seven movies in a fairly short period of time, so chances are, when he wasn't making, a good amount of his personal time was spent preparing for... making movies.
Lastly, regarding the comment that "Lee had more tools," Ali was the very man that Bruce Lee, by his own words, feared. "I don't fear the man who has practiced ten thousand kicks, but the man who has practiced one kick ten thousand times." Ali had practiced a small number of punches thousands of times over against the heavy back, live training partners, and against opponents in the ring. 61 fights, 56 wins, 37 knock outs. Ali also had more range on his punches than Lee had on his kicks, so it isn't like Lee could pick him off at a distance.
These guys weren't creampuffs either. Ali beat George Foreman, whos record of 81 fights, seventy six wins, keeps him to only five losses, same as Ali, and with 68 wins by knockout. I very seriously doubt that Lee could have stood up to Foreman. In fact, I doubt that Lee in his prime could have stood up to Foreman when Foreman wasn't in his prime.
So to answer the OP, Ali by a longshot.
That is no disrespect to Lee. Lee was a fantastic man and brought about a great deal of innovation in the martial arts and did much to promote the martial arts in very positive ways. His early death is tragic, but just because he died young and has a legend about him doesn't change the statistics or reality.
Daniel