stock line in inputs generally are shit. That's why getting a audio to usb cable is what u should do. audio to usb means that the analogue to digital (A/D) conversion is done separately from the onboard sound card (which as i said is in 99% of the cases rubbish). it might cost a bit more (20$-ish?) but it definitely is what you want. plus getting one that is made for guitar means that itll take care of impedance matching, and thus u wouldnt need to chain in your "pedal".
You probably will find one at radioshack. If not, try looking in music instruments stores (ones that sell mixers and digital stuff too).
And plus try to get a good one (one that has a good AD converter), because thats the main issue here for quality.
Good luck, and happy jamming.
EDIT: On a different note, if you're serious about getting sound in (and out) of your computer in general, you could consider an entry level audio interface (say one with one guitar in and another mic in) such as
this.