The housing market may be on the rebound, but stocks are a superior investment than homes are, according to Yale economist Robert Shiller.

"If it's just an investment, [not for living], I would say the stock market," he told CNBC.

The Standard & Poor's 500 Index hit another record high Tuesday, closing at 1,598. Meanwhile, the S&P Case/Shiller index of home prices for 20 cities soared 9.3 percent in February from a year earlier, the biggest increase since May 2006.

Editor's Note: The Truth About the Economy — Government Documents Lead to Eerie Conclusion

"Stocks for the long run — the two century-long history — show a lot of amazingly good performance for stocks," Shiller said. "Maybe it won't be that good in the future, but I bet it's better than housing."

In the decade ended December 2012, home prices, as measured by the S&P/Case-Shiller 10-City Composite Index, produced an annualized return of about 1 percent, while the S&P 500 appreciated 7 percent, according to CNBC.

As for February's home price increase, "the recent run up in prices probably has a lot to do with the lack of supply," Mark Vitner, a senior economist at Wells Fargo Securities, told Bloomberg.

"The more attention that home price gains get, more and more people will realize it's a good time to sell their home."

When it comes to stocks, "Even though the overall backdrop isn't overly positive, the market has a strong underlying bid, where it wants to go up on earnings and the Federal Reserve having our back with policy," Michael Mullaney, chief investment officer of Fiduciary Trust, told Reuters.

Editor's Note: The Truth About the Economy — Government Documents Lead to Eerie Conclusion