I agree with mb6
that more information is needed.
Since both shelters are fed from the same generator you most likely will have to bond the grounds together (even if it isn't "practical") for safety and code compliance reasons.
Where is the generator located relative to the two equipment shelters ?
Is all power locally generated all the time or is there also a utility grid connection with a transfer switch for the generator ?
Most importantly, what is the nature of the problem you are trying to solve ? The bonding of electric safety grounds is a completely different subject then ground loops on communication links.