Can't find him at any settlements, already tried the dog house method, ringing bells etc nothing works.

Without giving to much away, have you recently used him to track something down? if so, then he's probably still outside the last point to where he lead you if you didn't go inside, it's what happened to me.

Don't even know where I last saw/used him. Although, at Red Rocket it says I have one companion waiting there but there is none?

What did you do with Dogmeat... come on, come clean.! Is he on the dinner plate of some mutant right now because u needed a few more caps to by one more hit of JET!?!