Boy, you're arrival on this message board has appeared "to raise the dead" as it were. Postings here have been fairly sparse for some time. Thanks for shaking things up.
Any attempt to answer your query about identifying the "best" Union anti-bushwhacker unit would, I argue, be somewhat subjective. However, I will attempt to identify the most zealous Union anti-bushwhacker unit, and that unit would be the Fifth (Old) Missouri State Militia led by Colonel William R. Penick. This unit hunted bushwhackers with a tireless diligence that rarely, if ever, was equaled. At times they would go on long scouts searching night and day for guerrillas. They would wait in the brush for extensive periods in hopes of finding "bushwhackers." They would hunt guerrillas down at their camps and even force captured guerrillas to betray their comrades and serve as guides for them.
The vast majority of the officers and men in the Fifth were unconditional union men. Their main tenet was the preservation of the Union at all costs. They hailed from just about every part of the country and a goodly number of them were foreign born. The largest number of the foreign born came from German states.
"Some" of Penick's men were involved in thievery, thus the moniker Penick's Thieves. However, it should be pointed out that this conduct was by and large not supported by Penick or some of his officers. In fact, there are documented cases of Penick taking disciplinary action against troops who stole from the civilian population. On the other hand, Penick did deal harshly with guerrillas and their supporters. Much of this conduct can be largely attributed to atrocities committed on Penick's troops by guerrilla forces.
You might be interested in getting your hands on a recent work by Major Clay Mountcastle, who has a PhD in History from Duke University. The title is "Punitive War: Confederate Guerrillas and Union Reprisals." In it Mountcastle asserts that guerrilla warfare was the primary force behind the hard war conduct of Union troops towards southern civilians. Moreover, he argues that the hard war policy began in Missouri during the early stages of the war.
I hope this helps, Leonard. Let me know if you need anything else from me.
Larry L. Dishman