Figuratively is the broad term: not literally, covering every kind of non-literal language. Metaphorically is narrower and refers to metaphor specifically. All metaphorical language is figurative; figurative language also includes simile, hyperbole, irony and personification.
The core difference
A category and one of its members.
- figuratively — any non-literal use: metaphor, simile, hyperbole, irony.
- metaphorically — by metaphor specifically: one thing described as another.
Which to use
If you are flagging that a statement is not literal, figuratively is the safe word. Use metaphorically when you specifically mean the comparison is a metaphor — otherwise you are claiming more precision than you need.
The literally problem
The reason people reach for either is usually to correct literally, which is widely used as an intensifier meaning its own opposite. That use has been current for over two centuries and appears in major dictionaries, so it is not new — but in writing where precision matters, figuratively remains the word that says what you mean.