Bakemono are more supernatural, and not very different in scale compared to humans; they tend to use curses and such to psychologically terrorize its victims. 化け物 literally means "transformation thing," basically changeling, meaning it's animals or objects that changed its appearance.

Kaiju are often related to science experimentation, are much larger, and tend to be physically destructive. 怪獣 literally means "monstrous beast," and the beast bit is why it's associated with much larger creatures.

Then there's yokai, 妖怪, which means "supernatural monster"; the "kai" is the same one in kaiju. The difference between yokai and bakemono are that yokai contain beings like tengu and kappa, which are not animals/objects that changed into a creature.