Sometimes, column chromatography of extremely polar molecules is not straightforward even with solvent mixtures that contain MeOH - and let's not forget that methanol can partially dissolve regular silica gel. In these cases, you may wish to consider alternative sorbents for chromatography that are less polar than normal silica gel.
Examples include the following:
1) cyano-functionalised silica gel (you can use this as a normal phase or as a reverse phase, depending on the solvent mixture that you employ; it is excellent for the chromatography of polar molecules)
2) Florisil (this is a magnesia-silica gel that is particularly useful in the separation of lipids, steroids, vitamins, complex alkaloids and generally for polar molecules)
I hope this helps