There's still value to be found in the small-cap stock rally, Beth Lilly of Gabelli Funds said Wednesday.

"We look at the businesses from the ground up, and the companies that we talk to, we see business momentum is improving," she said. "As we look through the valuations and we do a sum-of-the-parts private-market value with a catalyst, we are still finding inexpensive stocks to buy in the market today."

The Russell 2000 index of small-cap stocks hit a record high for the second day in a row.

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Lilly, portfolio manager of the 5-star-rated TETON Westwood Mighty Mites Fund (WEMMX), said on CNBC's "Fast Money" that business sentiment was more positive than it had been six months ago.

"We're encouraged that things are improving," she said.

"We like to think that the companies that we invest in are Rodney Dangerfields on their way to becoming Bob Hopes."

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Lilly's top three small-cap picks were:

SunOpta, a natural- and organic-foods company that was selling off non-core assets.

Lilly said the company should see operating margins increase from 5 percent to 8 percent and shares climb from around $9 to $13 or $14.

SurModics, which makes coatings for medical devices, has a robust lineup of new products set for release.

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"They've got cash on the balance sheet, and an unbelievable CEO that is very focused on surfacing value," Lilly said.

BioScrip, a home-infusion company for patients with cancer or multiple sclerosis, was the third-largest player in the space with a CEO, Rick Smith, who previously has grown similar companies.

"We think this is an $8 stock on its way to $16," she said.

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The company recently lowered its forward guidance, which led to a dip in its stock price tha Lilly saw as a buying opportunity.

"Wall Street is very short-sighted and can't look much beyond next quarter, and he cut guidance, and Wall Street didn't like it," she said.

— By CNBC's Bruno J. Navarro. Follow him on Twitter @Bruno_J_Navarro.

— CNBC's Katie Young contributed research to this report. Follow her on Twitter: @katiecnbc.

Trader disclosure: On Sept. 25, 2013, the following stocks and commodities mentioned or intended to be mentioned on CNBC's "Fast Money" were owned by the "Fast Money" traders: Stephen Weiss is long C; Stephen Weiss is long BAC; Stephen Weiss is short JCP; Jon Najarian is long AAPL; Jon Najarian is long JPM; Jon Najarian is long FB; Jon Najarian is long MSFT; Jon Najarian is long MAKO; Jon Najarian is long BIOS; Jon Najarian is long DRYS; Jon Najarian is long BX; Jon Najarian is long NS; Jon Najarian is long NFX; Jon Najarian is long NAT; Michael Murphy is long BAC; Michael Murphy is long C; Michael Murphy is long JPM; Michael Murphy is long JCP; Pete Najarian is long AAPL; Pete Najarian is long calls C; Pete Najarian is long calls WFC; Pete Najarian is long calls INTC; Pete Najarian is long calls YHOO; Pete Najarian is long FB; Pete Najarian is long SBUX; Pete Najarian is long calls MSFT; Pete Najarian is long BX; Pete Najarian is long calls NS.