I think overall it's a tossup really, though it's tough to tell until they are in the ring together. Pacquiao appears to be faster on his feet, Mayweather appears to have better handspeed. But Pacquiao is darting in and out far more often, and Mayweather throws 1 or 2 quick shots at a time as opposed to the combinations Manny throws. Manny's also throwing with more power.
I think when pac unleashes that very quick 1-2, the left hand comes faster than any lead rights Ive ever seen from Mayweather. I saw the JMM 2 KD yesterday and had to super slow motion it to see actual left hand travelling towards JMM's chin. Its quite deceptive to look at because he throws so many punches, he cant have every shot thrown with full commitment to speed. Floyd on the other hand is such a pinpoint puncher than he waits for the opportunity, and when it presents itself he commits that counter with full speed. punch per punch PBF probably throws on average the faster single shots. Pac throws so many the odd one can be extremely fast, some can be average but he can throw fast combinations like no other.
Floyd has complete control over every inch and movement of his body. I'd say Pac has better basic hand speed and foot speed... but Floyd is a freak. He's like a rubber band or something. No sooner is he stretching out to duck or dodge a punch than he is snapping back with a perfectly timed punch of his own. Never seen a guy move like that in the ring. While Pac's speed is more conventional, Floyd almost seems like a shapeshifter.