So here it is. I've decided to crunch the numbers and let you know what the best thing to farm to make money. Now, this guide is going to assume that you, like the vast majority of people, do not own a melon sword. Therefore, you would need to rent one and this severely cuts into profits such that melon swording is not optimal. Mostly this is done because I don't own one and can't test it out.

So HERE IT IS! The contenders:

Netherwart Farming (since carrots/potatoes are worth less).
Cocoa Farming.

First Netherwart Farming.

This takes 1 unit of time to replant (even assuming a high herbalism level, you would still need to travel over most of the blocks which is what causes the time crunch).
It takes 1/2 of a unit to time to Fortune 3 harvest. (If you can't figure out why, this guide may not be for you)
If you have Fly, it takes 1/4 of a unit of time to Fortune 3 harvest (assuming ideal setup).
Total time: 1.5 units time (without Fly). 1.25 units time (with Fly)

Netherwart is worth 35 cents to the server. You will not sell large quantities to anyone else for more. Therefore we will use this price. Fortune 3 gives approximately 3.5 netherwart/block (assuming 0 replant, so you lost 1 netherwart/block for replant). 1 block = 1 unit space.
Total Netherwart gain: 3.5 NWart / unit space
Total Monetary gain: $1.225 / unit space

Now Cocoa Farming.

This takes 1 unit of time to replant. It takes an indeterminate time to harvest (if you're brilliant, it takes ~0.25 or less units of time to harvest, again improvable with fly or clever design). Again, this is not a farming set-up thread.
Total time: 1.25 units time or far less

Cocoa is worth 60 cents to the server. We will use this price.
Total Cocoa gain: 2 Cocoa / unit space
Total Monetary gain: $1.20 / unit space

Those of you bad at math will say that Netherwart is clearly better. However what we need to do now is some division! We shall divide total monetary gain / total time for each to get:
Netherwart: $0.817 / per space per unit time
Cocoa: $0.96 / per space per unit time (or more)

Netherwart w/ Fly: $0.98 per space per unit time.

Therefore, without Fly or High Herbalism level, cocoa is better. With fly it's about even. As your herbalism increases, Netherwart becomes better (up to $1.232 per space per unit time with Fly and Max Replant)

**I don't have fly yet so I can't test exact cocoa harvesting timing under those conditions, but I'm almost certain it will be better than Netherwart with Fly. Donations accepted.**

**Donations towards melon sword or its rental also accepted**

 

Well see, this thread is guaranteed numbers, irrespective of speed or other factors. "Pure math" we can call it.

In order to compare these to other farming methods (i.e. pumpkin/melon) would require actual timed trials in order to properly judge their worth. In the near future, I'll try to run said trials in order to assess with finality the best farming method (in $$/hour). I do have a pumpkin axe, and am about to get Fly/speed (soon as there's a sale) so those trials will also include some netherwart/cocoa numbers.