Oh. Well if you just wait for one of them to charge you, mid charge they are completely vulnerable. No phasing. It worked really well for me. If it started charging its bolt, I'd just give it a half charged shot, which would provoke it to charge. Freeze them in one shot, and shaaatter.
Oh, and the gear puzzle in question (unless I'm thinking of a different one... which I really don't think I am) is the one where you need to find an adequate vantage point to grapple from, flip the thing in the air, then blast it onto the axle with a missile.