What version ESXi? On the latest 6.0U1, the webclient can erase partitions on disks. Click Host->Manage->Storage->Storage Devices->All Actions->Erase Partitions
On other versions, I have been able to wipe drives by using the thick vSphere client and creating VMFS partitions on the drives and choosing to wipe/use full capacity of the drive for VMFS, then delete the VMFS partition.