If your ESXi are being managed by vCenter you can enable SSH with PowerCLI:
1. Open PowerCLI
2. Connect-VIServer <myVC>
3. Get-VMHost | Get-VMHostService | Where Key -EQ "TSM-SSH" | Start-VMHostService
To stop it:
Get-VMHost | Get-VMHostService | Where Key -EQ "TSM-SSH" | Stop-VMHostService -Confirm:$False
I believe you need to create a Read Only user for your ESXi servers with read only permissions, since Nessus need to access OS and it cannot do it from vCenter.