I'd suggest you migrate the vCenter Server VM over to the new cluster, then upgrade VMware Tools manually, and as a last step consider upgrading the virtual machine hardware. For the last step - if you are going to do this - I'd recommend you select the vSphere 5.1 compatibility (HW version 9) instead of 5.5/10. This will allow you to still manage the vCenter Server VM from the Windows based vSphere Client if required.
André