Star leg-spinner Alana King snared 5-19 and opener Phoebe Litchfield top-scored with 68no to headline the nine-wicket win on Friday morning (AEDT) in St Kitts.
Molineux did not play in the last two games of the tour, her first as captain, because of an ongoing back injury.
She now has several weeks to recover ahead of Australia returning to camp in May, ahead of the T20 World Cup from June 12 in England and Wales.
Molineux's injury meant she only played as a batter in the three T20s and then the first one dayer, before being rested.
But it did not matter as Australia dominated the six-game series. King said their new skipper had still made a strong first impression in charge.
"It's just a great character who's leading this incredible team," King said.
"Disappointing, no doubt, for her that she had to sit on the sidelines for a couple of games.
"But we're doing everything we can and she's doing everything she can to be ready to go when that World Cup comes around."
King was player of the match for her outstanding 10 overs, the spinner's second-best figures in an ODI.
The West Indies were bowled out for 136 in 35.4 overs, with Chinelle Henry 42no and opener Hayley Matthews scoring 34.
The home side lost its last five wickets for 21 and King took three of them.
After Georgia Voll was dismissed for 23, Litchfield combined with Ellyse Perry (33no) and Australia cruised to 1-137 in 19.4 overs.
"We're really pleased with how we finished the series. The T20s were quite commanding for us and we wanted to continue that momentum into the ODIs" King said.
She added it was important to Australia that they not back off in the last game.
"You can see sometimes in other teams, that the standards might drop. But that's what we pride ourselves on, we want to be the best team in all facets of the game," she said.
"We were just very clinical. We nailed our lengths and we owned that, then were able to bowl where we wanted to bowl.
"To reap the rewards was great, but the whole bowling unit did a really incredible job."
Some of the team will head to New York to start their break, while King is looking forward to her brother's wedding.
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