The mbrscan and mbralign tools need to be installed on the service console of an ESX machine (not esxi as it does not have a service console) or a helper VM if it can access the storage.
As you are running block level storage a helper VM is not useful to you as it cannot access your storage (Even if you passed it the LUN's it would not know what to do with VMFS)
Looking at other threads like this http://communities.vmware.com/thread/263820;jsessionid=95EB63CD3D05C808AAE0B10DB5686502?tstart=0 some people are putting in an ESX box temporarily and attaching it to their storage to perform the alignment work.
Other than that I have not been able to find a work around for block level storage and ESXI other than a temporary full blown ESX installation.
What you COULD do if your licensed for NFS on your filer, even if you don’t want to use it for your production storage protocol is make a temporary NFS volume, storage vmotion the target VM’s over to it (thereby making it accessible to a helper VM) align it and storage vmotion it back.
Other than that I am not sure if any of the other 3rd party alignment tools out there can interface with an ESXI box.
