I’m not sure I understand. iTunes (at least recent versions) does NOT store photos, it only syncs them. Unless you’re talking about album cover art, which it does store.
iPhoto is usually where the photos go, and you can delete them from within the program. Select the photo and choose “Move to Trash” from the “Photos” menu.
The actual files are probably in <your directory>/pictures/iPhoto Library somewhere – you can delete them from the finder, too.
It’s also possible you’ve just got a folder full of photos lying around, and iTunes can sync from that, too. Those you’d just have to find and delete from the finder.
If the photos came from the device, you’ll need to get rid of them from there, too. In iTunes, choose your device (button next to “iTunes Store” in the Library), and there will be a line of tabs across the top. One of them is “Photos”. The very first thing on that screen will be a “Sync Photos” checkbox. Either uncheck it, or else uncheck the album the offending photos are in, and hit “sync” in the lower right. Or just erase the device and re-sync it to your system.