Asked on "Squawk Box" if he were to invest a dollar in either company, Thiel said he'd "probably still go with Google" despite the antitrust concerns from European regulators.
The European Commission is pushing Google to make adjustments in its settlement over demands that the company make additional changes to its search algorithm.
"The risk with Google is the EU antitrust stuff," Thiel, an early Facebook investor and founder of the VC firm Founders Fund, said in a wide-ranging interview.
"Silicon Valley is sort of fairly oblivious to how this [antitrust issue] is building up because there's been very little scrutiny from the U.S. on Silicon Valley," he continued. "The EU is quite hostile. It's in part because European companies have not been able to compete on the IT sector. So they are running to the regulators to shut down the U.S. businesses."
The risk with Apple would be that the company, at some point, might lose the pricing power on smartphones, said Thiel, adding the tech giant's newly announced mobile payments system and the Apple Watch are not enough to make a difference to the company's bottom line. "If you have $150 billion coming from phone revenues, it's really hard to have product lines that even come close to moving the dial."
"Even the iPad wasn't enough to move the dial," he said.
"Maybe if they reinvent television sets, which is a thing they've been talking about for a long time, that might be a vertical that would be big enough," Thiel said.
—By CNBC's Matthew J. Belvedere