Fatty acids analysis - in the presence of 90% water.

[HW Mueller]

Going back to the original post´s GC problem: Diazomethane tolerates some water. I did thousands of diazomethane derivatizations, but since it worked very well I never investigated how much water can be present, I only know there was some.
On acid catalyzed esterification: Its a equilibrium reaction, one can easily estimate how much MeOH is needed to have a satisfying amount of ester.

[mckrause]

This is an easy analysis, without derivatization, on a polar column. Use a low-level split injection (or on-column, but split is better). The water is your injection solvent - use small injection volumes (1 uL or less). Rapid temperature program, probably 25 C/min or more. You'll separate them with no problem. I'd probably use some packing in the injector liner - consider a Restek split liner or something similar.

Calibrate in the same matrix.