This issue somewhat depends on what you're doing with the USB ground. See How to connect USB Connector shield? for a fair discussion, and http://forum.allaboutcircuits.com/showthread.php?t=58811 for more.

If the USB shield is not under your control and is tied to ground on board 2, or if you opt do tie it to board 2 on your own, then your choice is already made. You can't tie the shield to board 1.

My choice, in any case, would be to tie the shield to board 2, through a ferrite bead.

This issue somewhat depends on what you're doing with the USB ground. See How to connect USB Connector shield? for a fair discussion, and http://forum.allaboutcircuits.com/showthread.php?t=58811 for more.

If the USB shield is not under your control and is tied to ground on board 2, or if you opt do tie it to board 2 on your own, then your choice is already made. You can't tie the shield to board 1.

My choice, in any case, would be to tie the shield to board 2, through a ferrite bead.