OK, here's a spreadsheet image from a comparison I did on a recent save game. I was playing TAM 2.3, Large Med map, as Rome on Emperor. The save was from 140BC, IIRC, I had just clicked through 6 turns of anarchy, saved, then hit end turn and selected different governments and got the stats, without optimizing, so your results could vary!
At this point, I controlled all of Italy, all of the former Greek (Mycenaean) lands, the nearby islands (Sicily, Sardinia, Corsica, Crete), and had begun my invasion of Carthage, with about half their cities, so I was definitely seeing some max corruption at the frontiers. I had already built the Pantheon and Forum Romanum (Republic only) to reduce corruption, and about half my towns have courthouses, at least those that could get to 2-3 shields with it. No City Guards yet, though.
In the spreadsheet, I listed how many towns/citys/metros, my unit count and building maintenance cost. Then I listed the stats for each government type on the first turn out of anarchy. Total trade from cities is from the F1 screen, as is the corruption amount (shown below). Note, that the trade from cities amount is the non-corrupt total, so don't subtract the corruption amount, I just included those numbers and % as a comparison. The shields total is from the F11 screen, as total MFG = total non-corrupt shields.
You can see that Net Income, (whether in science or taxes) is comparable between Republic, City State, or Merchant Oligarchy. The trade bonus applies to all three, even though total corruption is higher in Republic. Note that I had been running Republic before the test, so my cities are 'optimized' for Republic, with core cities having most trade/science improvements to multiply the income there, while larger outlying cities do not. Given time to optimize the trade buildings for communal corruption, I think they would both improve. Sheilds, on the other hand, is a big difference. The communal govs give 62 more shields per turn, an increase of nearly 20%, and that's even with Smithy/slave markets in my core cities. For any large empire, I think that the communal govs are going to be more effective in the long run. Between the 2, I tend to think Merchant Oligarchy would be better unless you are a total war monger. As you can see, the savings from building maintenance makes up for the extra unit costs already. And this is a little misleading, as I have Temple of Zeus, Mil Training, and Harbor of Carthage, so I'm already not paying maintenance on harbors, barracks, or temples. Add those in, and you'd see a bigger difference in favor of Merch. Oligarchy. They also get the fastest workers, so I could afford to merge some more of those in and reduce unit costs.
Also see the note on Empire, with the first-turn forced resettlement, it's not a very accurate comparison, but I'd have to play them each through another 20 turns or more to bring the populations back in line, so I wasn't really able to test it. The unit support is HUGE, even with fewer cities/metros, but the lack of trade bonus is more than enough to offset that. Oddly, it seems that Empire would be good for a smaller empire trying to support a large military, the other govs seem to be able to support a decent military as long as you get enough cities.
Anyway, just some quick analysis, let me know if you spot any mistakes or have any questions! (BTW, I'm still in Republic for now in my real game, but I may switch to the Merchants after looking at this!).