Head to head, would a 200 lb. Joe Lewis have a chance against at 6' 9" with a 85" reach Tyson Fury? - yes, a 6 feet 2 inch, 204 lbs Joe Louis would certainly have an excellent chance of beating 6 feet 9 inch, 260 lbs Fury.
Of course, I could ask a similar question: Would 210 lbs Muhammad Ali have a chance against 6' 9" Fury? Yes, of course Ali would have a chance.
You can't say there'd be no comparison simply because Fury is a big guy.
Do you remember 7 feet 1 inch, 300 lbs Nikolai Valuev? Well, 6 feet 3 inch, 215 lbs David Haye outpointed the gigantic Valuev.
Although, I agree with you to an extent, it is difficult to compare fighters from different eras. One aspect to consider is their fight records, what records they set, etc. In this aspect, Louis's 25 successful consecutive title defences stands supreme.