I've run into a pack of lakelurkers. I can't damage them underwater even with melee weapon. My companions stay in the water trying to damage them but the lurkes never surface. I tried switching Boone and ED-E to passive but they insist on fighting. Should i just reload, leave my companions somewhere and lure the lurkers out of the water?

I've shot them underwater using a sniper rifle before, I doubt they're invincible underwater otherwise.

When and if they surface enough for VATs to work I can get in a shot or two, but that was a long wait. I'm shooting at them with a service rifle, shotgun and cowboy repeater? Where'd you get the sniper rifle?

Pick one up from one the armories in the quest lines or from a gun runner shop south of freeside. The trick is to use vats to spot them (with 0% accuracy) then exit vats and immediately shoot since you're technically still targeting them and that should work.