Einhorn also took a dim view of the Federal Reserve's easy monetary policy.
"I think they're behind the curve in terms of helping the economy. It's like too much of a good thing. They're actually, I think, slowing down the economy, even though they don't realize that they're doing that," he said.
When interest rates increase, the economy would ultimately benefit, he said.
"I don't really concern myself that much with the exit (of quantitative easing) because first of all, if they did raise rates I think it might be bad for Wall Street, but I think it would be good for the real economy and everyday, normal people out in the world, and, ultimately, you'd have faster GDP that would come from that," he said. "So, yeah, there would be a little hiccup in the market, but I think that would be a good thing to have happen."
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In April, Einhorn issued a note that suggested a technology bubble was forming.
However, the hedge fund manager, with $10.3 billion in assets under management, clarified his view.
"So, people sometimes saw the coverage of that and said, 'Is Micron a bubble? Is Apple a bubble?' We're not saying that at all. We're long those things," he said. "But there are maybe 25, 50, 75 stocks in the market which I do think have completely disconnected from fundamental values, still, in the same way that they did in 1999 and 2000."
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Einhorn also added that the bubble existed on a smaller scale and has stopped inflating since spring. "And we're actually beginning to do well on some of those negative bets."
One of those negative bets — on Athenahealth, which Einhorn named in May as his latest short idea — "is working itself out," he said.
"It's a nice business. It grows at a reasonable rate. It should get a reasonable valuation. And yet it trades at about 100 times earnings, and that's if you exclude stock compensation. I think stock compensation is actually an expense," he said.
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Einhorn said that the company's most recent quarterly results, which it reported in line with Wall Street estimates, relied on an accounting change reflected in its 10Q filing.
"They accelerated some of their revenue," he said. "That's a sign of a company that's really kind of pushing on the edge to keep everybody happy and involved with their stock."
Meanwhile, Einhorn's views on such stocks as Apple and Micron have remained positive.
"I think Apple is right now working pretty much on all the cylinders. I mean, there's probably more good things that they will innovate and grow in the future, but right now pretty much everything they're doing is going well," he said. "The top line is growing. The margins are expanding. And the capital allocation, you know, the buyback, has made a difference. I think it added about 7 points to their earnings-per-share growth in the quarter they announced."
Einhorn said that Apple customers tended to make repeat purchases, while the company continued to pull people into its ecosystem.
The stock price, he added, was also attractive.
"If you net out the cash, you're about 10 times next year's earnings, which I think is remarkable for a franchise like this," he said.
Einhorn said he wouldn't "quibble" on whether Apple should be buying back more stock.
"The important thing is that they're moving in the right direction," he said.
A recent selloff in semiconductor stocks was "the kind of short-term movement that creates opportunity," Einhorn said, adding that he sold off some stock at a higher price and bought it back after it traded lower.
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Einhorn also talked about his stake in solar-energy company SunEdison.
"It's a very complicated financial situation, but it's a very simple story, and I kind of like the way that that goes together because the complicated financial situation mean that I think a lot of people misunderstand the company," he said.
Einhorn said that SunEdison's assets and business would take its share price toward $32 from its current $18 level.
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SunEdison stock was attractive after a decline that corresponded with the recent selloff in crude oil, he added.
"It was like a baby being thrown out with the bathwater with the oil prices coming down," he said.