Cranky = original DK
Jr. = Cranky's son
DKC DK = Cranky's grandson
While Jr isn't referenced, the manual for DKC explicitly states that Cranky is DKC DK's grandfather, which makes sense, since (assuming human years) he's portrayed as being in his eighties, while DK is supposed to be a relatively young whippersnapper, probably in his mid 20s or thereabouts. Wouldn't be normal for a guy Cranky's age to have a son in his twenties, more likely his son would be in his 40s to 50s.
I'm actually kinda surprised that they didn't have Jr show up in the DKC games, would've been funny to see how they'd handle that.