What's the difference between these two sentences?
I know that the particle は is used to topicalize things. Maybe when は is used, the sentence will have different meanings, not just "Eels are fish?"
The particle が, on the other hand, is used in neutral statements. Maybe this can be the case here?
Or even maybe it will be hard to say the difference between these two sentences, because additional context need to be provided?
Contrary to your expectation, ウナギは魚だ is usually the natural sentence that just means "An eel is (a kind of) fish". Topicalization is not a rare phenomenon at all in Japanese. It happens all the time when there is a need to convey some knowledge, like "My name is Alice", "Sparrow is the name of a bird", "This is a smartphone", and so on. Articles on Wikipedia almost always start with sentences that contain は.
ウナギが魚だ is also a valid sentence, but it makes sense only when you want to say "It's an eel that is a fish" or "Eel is the fish (among them)". This usage of が is called "exhaustive-listing が". You need to say this in response to a question like "Which is a fish, an eel or a dolphin"? Obviously, a sentence like this is needed much less often.
If you've heard something about "が for neutral description", this is not what you may be imagining. Please read this.
See also:
One of the factors that determines which of は and が sounds neutral is what type of predicate the sentence has. If it's either nominal or adjectival (i.e. if the sentence ends with either a noun or an adjective), は sounds neutral. In this case, you would be talking about a characteristic of something that is already known to the listener and therefore is suitable as a topic. が places specific emphasis on the subject it marks, as if to say it, and nothing but it, possesses said characteristic. So ウナギは魚だ is a neutral sentence about eels as a species, while ウナギが魚だ would make sense only as an answer to a silly question like ウナギとウサギとどっちが魚だ？
If the sentence ends with a verb, が sounds neutral when the new information to be conveyed is the whole of the subject doing the action of the verb. For instance, ウナギが死んだ would convey the fact that a particular eel died. は in this sentence would add a sense of contrast, as if to say that particular eel died but some other animal is alive. However, a verbal predicate may also be used to state a general characteristic of something just like a nominal or adjectival one. For instance, ウナギは死ぬ would be understood as stating the fact that eels die just like any other living thing, unless the context suggests that it’s a prediction about a particular eel’s destiny.
