I once thought there might in theory be a way to answer questions like this. Now I have no idea. You are talking about two guys close to, or at, the top of their talent pool, with no prime film between them. So the margin for victory is narrow, and probably depends on style and technical considerations. They both fight in styles that no forumite has ever seen or used live. Most of the assumptions underlying good technique in the 1880s and 1890s are long dead. Beyond that, our sources are mostly newspapers. How do we even reconstruct their styles with enough certainty to say how they fought, let alone who would be better at it?
Based on what little we know, you would have to make Sullivan favorite. Sullivan was a lot more dominant, and there was not what amounted to a paradigm shift between their eras. Also when you match two punchers, you go for the one with the better chin, if nothing else much separates them. Could Maher win? Sure, I just don't see any grounds for installing him as favorite.
I think that Maher's chin isn't nearly as bad as some people believe. He was stopped a total of 5 times before 1900 - against Jackson, Fitz and Goddard. After 1900, Maher was washed up with alcohol problems so I wouldn't judge him based on that period. Still, his fights with Fitzsimmons and Goddard suggest that prime Sullivan would be too much for him.
Interesting match up. I favor John L even though he never beat men as good as many who defeated Maher. Still he seems more durable to me.
...And Maher just retired against Jackson, not floored just outclassed as a virtual mature. Both hit hard, Maher probably harder, Sullivan probably quicker with better whiskers, while Peter beat better opposition, a pick-'em fight.
