I have an HP DL380 G5 with ESXi installed on a local RAID (146x3 RAID1) and it has attached an MSA60 storage. The server has issues so I will replace it with an identical machine. I know I will probably lose the local raid but what about the MSA60? If I replace the controller and put in the new identical server, will it be fine? Is the RAID for MSA60 on the BIOS?
It will be fine... HP RAID metadata is stored on the disks, not the server or controller.
If you're using identical equipment, moving the internal disks into another server will work. The MSA60 should be unaffected.
But remember that this is VERY old equipment. 10 year-old systems. I hope you're not running anything too critical on this setup.