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I see THIS as 3rd bubble in 15 years: Analyst Peter Boockvar

There's a bubble building in the bond market, market analyst Peter Boockvar said Thursday.

"This is the third bubble in 15 years. It's in fixed income," the managing director at economic advisory firm The Lindsey Group predicted in a CNBC "Squawk Box" interview.

"From what I'm seeing, at least over the past two months—that began really in Europe when the German 10-year yield has gone from seven basis points to 1 percent—is that air is slowing coming out of the fixed-income bond market," Boockvar said.

Read MoreIcahn: markets 'extremely overheated,' especially in junkbonds

Similarly, in the past two months, the price on the U.S. 10-year Treasury also sank—driving the yield 25 percent higher.

Last week, total bond funds saw nearly $4.1 billion in outflows—on top of a $2.9 billion exodus the prior week, according to the tracking group Investment Company Institute (ICI).

Since the beginning of the year, however, investors put $42.7 billion into bond funds, after adding $43.5 billion last year.

ICI total bond fund flows 2015 (in millions)

Monthly Jan 31, 2015 $10,100
  Feb 28, 2015 $17,193
  Mar 31, 2015 $6,321
  Apr 30, 2015 $6,837
Weekly May 6, 2015 $2,550
  May 13, 2015 $2,162
  May 20, 2015 $1,963
  May 27, 2015 $536
  Jun 3, 2015 $2,058
  Jun 10, 2015 -$2,897
  Jun 17, 2015 -$4,089
Total $42,734

"They have piled into fixed-income, and that's where a lot of the flows have been," Boockvar said. "Fixed-income is where they lie. And that's where the risk is if the fixed-income market started to [turn]."

On the stock side, retail investors have missed this entire rally, he said, because they pulled $60.2 billion from stock mutual funds last year and another $45.5 billion this year.

ICI U.S. stock fund flows 2015 (in millions)

Monthly Jan 31, 2015 $6,583
  Feb 28, 2015 $1,779
  Mar 31, 2015 -$8,783
  Apr 30, 2015 -$19,628
Weekly May 6, 2015 -$1,729
  May 13, 2015 -$5,053
  May 20, 2015 -$5,388
  May 27, 2015 -$2,872
  Jun 3, 2015 -$4,197
  Jun 10, 2015 -$2,769
  Jun 17, 2015 -$3,450
Total -$45,507

Those sobering ICI figures come against a backdrop of stocks trading around new highs. The S&P 500 was up 2.41 percent this year as of Wednesday's close. The index gained 11 percent last year and 30 percent in 2013.

"Retail [investors] have been burned by two bear markets in eight years. They're not rushing to get back into stocks, when they see potentially another bubble," said Boockvar, who's been rather cautious on stocks for a while now.

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