I'm not going to say that Mayweather isn't good or isn't even historically great at his sport. Nobody goes 48-0 at the top level of a combat sport because of luck. I do think however that basically his career comes down to a few factors:
1. He's a large fish in a small pond. He's never actually had to go through historically great competition like the best boxers of it's past had done. This was perhaps his biggest test, and lets be honest, Pacquiao is well into his decline and is starting to get washed up. It's not that impressive, and I don't see too many, if any, bouts in his career that have been impressive epically memorable wins people will remember through the years. I think the chance he probably dodged Pacquiao in his prime until now are pretty good also. For a historically great 48-0 boxer to only have maybe one historically memorable fight and even then only because of the circus atmosphere surrounding it and not because of action in the ring is pretty telling.
2. This goes along with point number one. Boxing, while it might occasionally generate good money on PPV, is at a low point for the sport since it started to become a major sport over a century ago. Most people, most casual fans even, probably couldn't even name any other boxer besides these two. That even goes for who the champs are let alone the high placed rank and file boxers. It's just not a sport most of the best athletes, especially in the US, want to get into anymore. Most people just don't care about it.
3. Even more than the above two points is that Mayweather might be the best of all time at manipulating the flaws in the structure and rules of boxing, especially in the modern day. At one time it was supposed, or at least thought, to simulate actual fighting. It doesn't. The thought it does is laughable. (MMA is more than proof of that.) Boxing doesn't have much real world correspondence to a real fight. Even not taking that into account modern boxing doesn't even coincide to the spirit of what it was supposed to be when it sport was created. It just wasn't meant to be a sport where somebody dances around all day evading and playing a defensive battle in the hopes of beating out the opponent by decision on points, or if we're being very generous slowly wearing out opponent to then beat them another way, instead of actually engaging the opponent. Mayweather is the best at doing that. That the boxing organizations and the athletic commissions have been so hidebound and corrupt not to change the rules (along with many other aspects of the sport) doesn't change the fact that boxing now is what it is.
So is Mayweather one of the best if not the best of all time in what boxing is? I would say yes. Is Mayweather one of the best at what boxing is thought to be throughout it's history and should be? No. He certainly isn't a "fighter", even by boxing standards. Boxing has only slightly more in common with actual fighting than tennis or volleyball now. He’s much more athlete than fighter. He's an athlete that has become very good at a flawed sport. One that's flawed both inside and outside the ring.