Is there a way to crop using a specified pixel box?

Yes, there is. On the Capture ribbon tab, look into the "Region Setup" part - click into the box that says "Size: Any" and select 640x480, or anything you want. Then use the Region capture command (Ctrl+Shift+R) to capture from the screen the rectangle of exactly that size. You can open your original images in any image viewing software. If you want to re-capture them from HyperSnap window itself, in-check the "Hide window" option on the "Capture" ribbon tab, so that HyperSnap window is not hidden when you capture screen.
 
Greg

Set magnification to 100% in HyperSnap to see the image in its natural size. Otherwise it may show your image in enlarged or reduced size to fit it into its window. If upon pressing the region capture hot keys or starting region capture in any other way it seems that everything on your screen is getting larger, you are probably using an old version 7, or one of the earlier versions 8.xx of HyperSnap under Windows 7, 8 or 10. In such case it's best to upgrade to the latest version 8 of HyperSnap, which is fully aware off all new versions of Windows screen resolution settings.
 
Greg