Unless your vinyl is extremely noisy, so many clicks and pops that you hear more of them than music, I'd not use any software cleaning. Any declicking you do will have audible effects on the music. Also the better built the turntable and cart, the less likely the clicks and pops will bother you. Now if this is something rare, that you need the cleanest sounding results possible, I would remove the clicks and pops manually. Software such as Adobe Audtion will let you do this.
Here's what I do when transfering vinyl:
First I clean the LP on a VPI 16.5 RCM. I also use a quality turntable/cart/preamp combo (VPI,SHURE,Dynavector) and a quality sound card (m-audio audiophile firewire).
You can use any sound recording program, if going to cd, I'd record straight to 16/44khz, if archving for digital storage not on cd, go for 24/96 then compress to a lossless codec such as flac.