At an "award ceremony" on the sidelines of the World Economic Forum in Davos, the Swiss chapter of Greenpeace and the Bern Declaration said Goldman Sachs had won the jury prize, while Shell had been chosen by online voters for the public award.
Goldman Sachs "is a key player in financially driven globalization, which pays for profits of a few with exploding inequality and the impoverishment of broad strata," the groups said in a statement.
They highlighted the investment bank's role in the Greek debt crisis.
"Goldman's derivative deals, which fudged Greece's way into the eurozone, pawned the future of the Greek people," said Andreas Missbach, a financial expert from the Bern Declaration.
Shell won the public vote by a wide margin among 41,800 online voters, the two groups said, singling out its "highly risky search for fossil fuels in the fragile Arctic".
"Shell has invested $4.5 billion into a senseless, highly risky plan and only produced problems. Greenpeace International director Kumi Naidoo said.
"The Public Eye Award vote shows that the public keeps an eye on Shell and that its pig-headedness will continue to be sanctioned by public opinion."
The groups have carried out the "naming and shaming awards" at the annual gathering of the world's political and business elite in the Swiss ski resort of Davos since 2000.
Last year's winner of the jury prize was Britain's Barclays bank, while the public award went to Brazilian mining giant Vale.