There certainly isn't much on this song in the Traditional Ballad Index:

Pay Me My Money Down

DESCRIPTION: "Pay me, O pay me, Pay me my money down... Pay me or go to jail. Pay me, mister stevedore.... You pay me, you owe me...." Almost anything may be included, but all on the theme that the boss has hired the worker and should pay him for his labor
AUTHOR: unknown
EARLIEST DATE: 1944
KEYWORDS: work money nonballad
FOUND IN: US(SE)
REFERENCES (4 citations):
Lomax-FSNA 279, "Pay Me" (1 text, 1 tune)
Hugill, pp. 501-503, "Pay Me My Money Down" (1 text, 1 tune) [AbEd, pp. 370-371]
Silber-FSWB, p. 83, "Pay Me My Money Down" (1 text)
DT, PAYMONEY* PAYMONY2
CROSS-REFERENCES:
cf."Tie-Tamping Chant" (floating lyrics)
cf. "Darlin' (I)" (floating lyrics)
File: LoF279

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The second Digital Tradition version is the one I've heard most often. These are almost exactly the words used by the Weavers. Sing Out! Reprints (1959) says “words & music by Lydia Parrish (wife of artist Maxfield Parrish). TRO Copyright 1942 (renewed) Hollis Music Co., NY). From Lydia Parrish, Slave Songs of the Georgia Sea Islands (1942; University of Georgia Press, 1992, pp. 208-210; with music). But as you can see in Barry Finn's post above, the version that came through Lydia Parrish is a bit different.
This version is also the one posted on various Grateful Dead Websites. Jerry Garcia sang these lyrics in 1962, playing banjo with an unnamed bluegrass band.

PAY ME MY MONEY DOWN (from Digital Tradition)

cho: Pay me, Oh pay me,
Pay me my money down,
Pay me or go to jail !
Pay me my money down.

I thought I heard the captain say,
Pay me my money down,
"Tomorrow is our sailing day."
Pay me my money aown.

The very next day we cleared the bar,
He knocked me down with the end of a spar,

I wish I was Mr. Howard's son,
Sit in the house and drink good rum.

I wish I was Mr. Steven's son,
Sit on the bank and watch the work done.

@sailor
filename[ PAYMONY2
RG

So, we've established that the second Digital Tradition version is that one published in Sing Out! Magazine in 1959. This exact version is also in Folksinger's Wordbook (Silber & Silber, 1973)

The first Digital Tradition version puzzles me. I haven't found a source for it. Here are the lyrics we have:

PAY ME THE MONEY DOWN (from Digital Tradition)

Pay me, O pay me the money down
Pay me the money down;
Pay me, O pay me the money down
Pay me the money down;

I went for a cruise, boys, around the town
And there met a young gal called Sally Brown

I put me arm around her waist,
She says, "Young man, you're in great haste."

That fancy girl, she says to me
"I don't give my love for free."

"Oh the price of my love is half a crown
Pay me, O pay me the money down."

That girl she says to me one day,
"You've had your fun so don't delay."

"Oh money, young man, is the object of me
And you won't get my love for free."

She said, "Me son, you'll rue the day
The girls have worn your pride away."

@sailor
filename[ PAYMONEY
TUNE FILE: PAYMONEY
CLICK TO PLAY
RG

Can anybody identify the source?