Isolators are the better choice IMHO. They keep the two batteries separate, so if one goes dead it doesnt take the other one down with it. Relays can accomplish the same thing but have more moving parts so hence are more prone to failure
and the batteries are actually electrically connected to each other when charging. With an isloator they are never connected together, they are protected from each other by "big honking diodes" or something very similar
If you add a relay, I would go with a starter relay. It will handle the power of a "jump start" and is fairly cheap. I would also go with a momentary switch to close the relay. That way you wont forget and leave it on
thus bypassing the isolator.
I guess one of the the main differences is the price. Relays are about $15Cdn while isolators run around $80Cdn.