Even though Franky is a better character, I think Queen is a better Cyborg. The guy replicated almost all of Germa's tech, he can do most of the things Franky can do, but better. (Radical beam, rocket launchers, etc.) Sanji would dog Franky, but Queen was going toe-to-toe with him, using mostly cybernetics. The only notable powers Franky has that Queen does not are Nipple Lights and Coup de Burst/Vent. Franky can use the pacifista light beams, but he requires charge up, and Queen was just casually throwing them out. In a battle of pure cybernetics, I'm giving it to Queen.
(Note: I'm not including external devices Franky built, such as BF-38.)