In a way, Maxwell’s equations are the first that specifically deny ether. Maxwell came up these equations the describe electromagnetism very well, but aren’t invariant under Galilei transforms. In particular they describe electromagnetic waves that travel at some speed “c” – Not “c relative to some reference frame”, just “c”.
The conservative thing to say was “well, Maxwell’s equations must only be right in some reference frame (at rest relative to the ether)” and start looking to figure out what that reference frame was. As we know, that search failed, and with relativity we essentially said, “Maxwell’s equations are even better than expected, because they are true in all reference frames, not just some preferred one”.
Maxwell’s equations were made at a time when ether seemed sensible, but got better thereafter.