gravel clean

I clean the top of my substrate every two weeks or so, but I never really messed with the bottom part since I read it can be detrimental. It was getting bother by always having to clean algae off the top of substrate (it doesn’t appear everywhere, just some areas), and decided to put a lantern...

Our 125 frag tank has crushed coral gravel as substrate, chunks are about 10-12mm in size. Sand sifters are probably a no go, what can I put in here that will clean the substrate? I am unable to gravel vacuum it without taking all of the egg crate out which houses our frags. Pics of the algae.