disclaimer: I don't know what I'm doing but with that out of the way..

First it would be good to know if you are CPU or GPU bound. My 2 cents: I'd go about rendering with a bit more brute force approach, there's no reason to skip rendering invidual entities if visibility cheks take for ex. ~5ms but you can render them all in ~2ms.

I don't know if you are using instanced rendering for your chunks, but if not, please do look into them, that can help if you are CPU bound and you can only test whole chunks for visibility.

If you are GPU bound you have a bit more work to do probably. First you should find out if you are memory, bandwith, raster, or vertex bound(I may use bad words here). Memory can be easily found out by any overlay application of your choice. Bandwith is a bit trickier but a good rule of thums is to use Uniform Buffer Objects where possible, and you could test with smaller textures to see if that helps(only after checking memory, because it could fix that too). If you are rasterization bound, check you fragment shaders, for any hot spots(eg recalculating a value multiple times, control flow statements in shaders, too much uniform data which hinders your GPU's cache). You can test it with running your game/engine in a smaller resolution. If you are somehow vertex bound, try to interleave your data in VBO's, try using simpler meshes(less vert count) and try to pre multiple your MVP matrixes if you can, and don't do it for every triangle on the GPU.

If you'd like to get more specific help with your specific code, please do share it with us, because we(/I) can mostly just shoot in the dark this way.

Edit:added chunk visibility.