I would try doing HPLC using a 25 cm C18 column with a gradient from 5 to 100% acetonitrile for a beginning. Depending on how many compounds have to separate it might be unnecessary to run on such a long column and 15 cm could work fine. UV-diode array detection is marvelous for flavonoids because you can quantify various kinds of flavonoids at different wavelengths simultaneously.
Yes, column chromatography would be ideal for your purpose. Prepare the column in chloroform and use the solvent system chloroform:methanol (8:2) or other proportions selected after TLC screening. Monitor the fractions using the same solvent system for repeated TLC of fractions obtained. Pool the fractions with single spots, concentrate them and allow them to crystallize in a refrigerator. I hope you would get positive results.