I did a timed test of nearly identical 200 2 blocks wide melon and pumpkin rows and timed them, here were the results:

Melon: 360 melon and $540 2 minutes 54 seconds
Pumpkin: 417 pumpkins $312.75 1 minute 54.3 seconds*

Overally it was pretty close but I'd say pumpkin was a bit better because the server was lagging while I was doing that

*Lagging during test

 

Pumpkins are better, but if there`s lag then melons are probably the way to go.

 

Pumpkins are way better.

Melons=12k with best tool
Pumpkins=20k with best tool and CJB and 16-17k without CJB

 

But you have to have fly and something other than a mac to use CJB

 

Melons all the way. Silk Touch that's $1.5 a melon as opposed to $ around .5 Asuming you have at least a 100*100 farm you won't have to worry about regen times.

 

MELONS

 

Have you ever seen how fast pumpkins break with an EffV axe? I assume not.

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This is an estimate of what I make on each crop per hour:

Melons: $12,000
Pumpkins: $18,000 (without using CJB or speed)

I'd say definitely Pumpkins IF you have access to a 200x200x3 farm AT LEAST (because of how fast they're harvested, entire floors will be taken out in a relatively small time) and have someone that can quickly get your items repaired (unlimited erepairs, someone selling cheap ones, etc.) Also, it's true that lag can really affect you when farming them, but there are some ways to avoid it and just keep going perfectly fine while still getting more money than melons. (EffV is relatively easier to get than a Silk Touch, as there are Eff4's everywhere and on average the most you'll have to pay for an anvil combination is 4k)

However, if you simply don't know how to deal with lag, or there is only a 100x100 pumpkin farm at your reach I'd say the answer is a definite NO. Another important thing to remark is that if you don't have erepairs (or unlimited e-repairs from a couple buddies) and can only farm with one Eff5 tool, you're gonna have a VERY bad time. I use 2 Eff5 axes, and still need to repair them quite often. Money loss isn't the problem in buying erepairs (you can get $300 a minute easily with pumpkins) but rather how sometimes it can take time to get someone to repair them quickly for you.

Though, I must admit that the reason I like to still farm Melons often, is their 'versatility'. It takes you a while to farm just a single 100x100 floor, and even odd dimensions as long as they are multi-floored can still work perfectly fine (i.e 60x80x3, 75x75x2, etc.) and of course, you won't need e-repairs nowhere as close as Pumpkins do as you'll most likely just need a single erepair per hour; and the profit still isn't bad at all. ;)

In conclusion (tl;dr):

Farm Pumpkins (even though they give more money) if you:
- Have access to a very big farm.
- Can get [cheap] and quick erepairs.
- Know how to handle lag.
- Have an EfficiencyV axe. (Pickaxes won't break pumpkins anywhere near as fast.)

Farm Melons if you:
- Have Silk Touch and at least EfficiencyIV on either an axe or pick. (Doesn't matter in this case.)
- Have Access to any dimensionally decent farm out there.