I would assume Alexander was referring to the Brotherhood of Steel.
The Crimson Caravan and Van Graffs are working against the Gun Runner's in general. It's not that the Van Graffs just wanted the GR's to stay away from Energy Weapons; they both have an "alliance" against all other caravans, so it's unlikely the Van Graffs would just stop their attacks if the GR's stopped transporting energy weapons.
Secondly, I think the Gun Runner's would put up a damn good fight against the Van Graffs in a fight, if not completely obliterate them. The Gun Runner's have the finest firearms and they're rather clever with protecting their caravans.
To me, it all points to the Brotherhood. No matter what precautions the Gun Runner's would take against attackers, the Brotherhood are the ones who would definitely KEEP trying no matter what, because for them it's not just a matter of business rivalry, but it's their BELIEF that the Gun Runner's shouldn't be allowed to own and trade high tech weaponry.
I'm more inclined to think it was the Van Graffs. I haven't played the first two Fallouts but from FNV I got the impression that the Van Graffs are energy weapon specialists - by attacking only the EW caravans the message the Gun Runners get is "stay out of the energy weapons business". If the Van Graffs just indiscriminately targeted all GR caravans the message the Gun Runners would have gotten instead would have been "someone is out to get us". This way the Van Graffs get to retain their EW monopoly, but don't piss the Gun Runners off so much that the Gun Runners are actively, uhm... gunning for them. The Van Graffs don't stand to gain much from attacking the non-energy gun shipments anyway, since they don't seem to deal in conventional guns and there doesn't seem to be an overlap between users of the two - it seems like you either prefer energy weapons or conventional guns.
I'm not sure the Brotherhood would have had enough intel on which caravans were carrying EW and which weren't. That the attackers were able to identify correctly all the EW-carrying caravans suggests, rather, corporate espionage, which in turn suggests the Van Graffs.