Pictures would be awesome.
Assuming things are 'okay'
Black grime sounds like a mold of sorts to me, not bacteria.
Careful 'soaking' in PBW in both containers, as it can cause dammage to both glass & plastic if left too long. I'd suggest make a little stronger than normal batch of PBW for the glass carboy, & scrub w/ a carboy brush. As for the Better Bottle, as long as the plastic isn't comprimized, fill part way with PBW (regular strength) & throw in a wash cloth. Put a solid bung in the top, and either rock the carboy on its side or shake vigorously 'forever'.