We often think about the independant generals or the Emperors leading their armies, but one must remember that during the imperial period many generals did many great acts without getting much publicity and without the ressources of a Caesar or a Trajan. One such exemple on which we are quite well documented ( when compared with other generals ) and who seems to have been a very competant general is Cnaeus Domitius Corbulo who lead, under Claude and Nero, armies in both the west ( retaliation campaing in modern Netherlands at the time of the invasion of Britain ) and in the east ( campaign in Armenia and Parthia ). He could contend in this poll.
Another general who could certainly be a serious contender is Lucius Licinius Lucullus, whose campaign in the east led further north-east than any other general of Rome and who was able to crush Mithridates VI with limited ressources in a rather small amount of time. His reputation was tarnished by political manoeuvring from Clodius but he must be considered one of the best generals of the late republic despite his unability to retain the fidelity of his men.
Finally a third name comes to my mind, that of Sertorius the rebel general who was able to best Pompey for years with very limited ressources too, in a campaign of a kind never seen before in roman history.