Automatically as viewers we know that Mr Upstairs is wealthy - I mean, in the first shot we see of him (watching the testimony on tv) he's in a rich room with what appears to be expensive furniture/paintings, is wearing a suit, and he has a servant. Contrast this to the longshoremen who are "poorer now then when [they] started" - the scramble to get the work tabs earlier on in the film - the financial struggles they face. Mr Upstairs is also physically higher than the longshoremen (never seen at the docks) and so he appears to be the character who wields all the wealth of the waterfront. Also we never get to see his face, we only ever see him from the back - he's not as involved in the film or the waterfront incidents and he's always just watching everything from high above - which shows him to be domineering and controlling of the entire waterfront.
I guess the question of "why" Mr Upstairs is given all the wealth and power in this film could have a lot of answers - I reckon it's because Friendly isn't so much the "super-villain" of the film; that role would go to Mr Upstairs. Kazan could've given Friendly all the power and wealth in the film - I mean, Friendly is villainous for sure, but he's controlled by Mr Upstairs - Friendly holds wealth but not to the point that he can control the entire waterfront (as we see in the end, without his minions he's got no control really). I think in a way Kazan wants you to feel sympathy towards Friendly in the end (a lot of essay q's focused on this last year too) because although he's the bad guy, there's a greater evil power above him in the form of Mr Upstairs who has more power and more wealth - so much so that he's not even attached to the whole waterfront scandal - he simply turns off the tv and walks off - I guess you could say that's an indication of just HOW MUCH power Mr Upstairs has over the waterfront