You can use bows the entire time for the lizards nest. I have managed to get them all every time except once where two escaped because I panicked. A good bow like everyone says (I didn't have a Sticky Compound +5 at the time so I used a Lava Bow), heavy arrows (not many really, expect 2 arrows per lizard unless your dex is really low, so about 50 heavy or even regular arrows should do but if it's your first time you should bring 100 just in case) and of course a Thief's ring.
First, if you start from the Armor Spider Archstone area, and go down the platform where you have to kill a minister, then expect the first two lizards to run towards the tunnel, into the nest and disappear so kill them quickly with whatever you have but don't give chase into the nest unless you're certain you can kill them right away. Afterwords, as you approach the tunnel exit into the nest, you'll see a lizard just hanging out so snipe him out really quick. Keep to your right but walk the entire way. As you exit, continue to walk to the right but slowly. You should see the glow of a lizard where the path splits leading down to the rest of the lizards. Keep an eye on him as you keep to the right. The moment he starts running, stop moving. He'll give up the chase after a few moments and start walking back. As he gets near his last location, he should fall into the pit where the rest of them are. At this point start walking to point where the path splits and snipe out the lizard that's at the bottom of the path. After, continue heading on the path that leads up, then when it ends carefully drop down to the wooden platform. Continue on and drop down to the crate below. Keep walking forward where you'll see some random dead guy next to a pile of three rocks. Walk back as far as possible, drop down and pull out your bow. From there you should be able to snipe most of the lizards out. You can move around a bit to adjust your point of view. Make sure you can hit them without a piece of wood getting in the way in case you need to adjust your aim for a second shot. I can guarantee getting all of the lizards as I'm doing it now as I type this up. Sorry this was so long but I hope it helps.
Update: There's a chance that one lizard may be hiding from your sight. In which case once you see that you have gotten them all, Get a sword or other weapon ready and chase him down. It won't have enough time to escape in such a confined space.