While biotech should have an "okay" year in 2013, both managed care and hospital stocks should put in another repeat performance in 2013 as Obamacare is implemented, Funtleyder said.
The S&P 500 managed care index, which includes UnitedHealth, Cigna, Aetna, Humana, Wellpoint and Coventry, rose nearly 5 percent year to date in 2012. The health care facilities index, which includes only Tenet Healthcare, surged more than 50 percent. Other hospital stocks like HCA were also up sharply on the year.
But the fund manager told CNBC that hospital stock performance could be more dependent on the economy than on Obamacare in 2013.
Managed care stocks may also trade sideways heading into 2014 when an estimated 30 million more Americans will have access to managed care under Obamacare, Funtleyder said.
—By CNBC's Justin Menza