I have to go with Caesar, not only because of the brilliance of Alesia, but because he proved superior siege capability in campaign after campaign.
Just some rough examples...
Alesia stands out, of course, but the Gallic campaign included several sieges.
Massilia in Narbonensis... essentially conducted by Gaius Trebonius, but its initial stages were directed under Caesar.
Petreius and Afranius (Pompey's Legates in Hispania) were essentially besieged, but on open land. Sure they were scared to face Caesar in open battle, but it doesn't change the fact that he essentially 'besieged' them into submission through maneuvering and bottling them up.
Dyrrachium.. despite losing the battle, Caesar nearly ended the 'civil war' without actually coming to major conflict with Pompey. Pompey was effectively maneuvered into an untenable position and besieged, but he did eventually show some backbone and skill and defeated Caesar's smaller army where the siege works weren't yet completed.
Alexandria showed Caesar's ability to withstand a siege while precariously undermanned.
The Republicans in Africa (who spent months delaying and avoiding battle with Caesar) were maneuvered into a 'no escape' stretch of land at Thapsus and fortified in, forcing them to do battle.. and be destroyed.