If you're a subscriber to MobileMe (the Apple cloud service) then you could save them to your MobileMe iDisk from your Mac and then download them on your iPad.
Or you could email them to yourself and download the email on your iPad.
I use PrintCentral - which allows you to WiFi transfer files from your PC/Mac to your iPad. GoodReader is another app that enables you to do this.
In all of these cases, when the files arrive, you'll be able to save them to iBooks. For example, if you were to email the PDF files to yourself then, depending on how big they are, the iPad mail program will either display them immediately or offer you the option of downloading them, where they will be displayed in the iPad mail program. In the top right hand corner of the display will be the 'Export' icon (curled arrow) and that will offer you the option to 'Open in iBooks'. If the arrow 'disappears' (to give you a full screen display) touching the screen will temporarily bring the option back again.
Tim
Scotland