The method of choice is to use higher pressure liquid chromatography(HPLC) after solvent extraction and purification. for IAA determination, you could read my published papers, such as that published in the French Journal,FRUITS,55,2000, IAA concentration during fruit development in Hillawi date palm.However, for cytokinins, which are basic in nature, as opposed to auxins, which are acidic,then you must change the pH to 8.5 of the aqueous phase, then do partitioning, using freshly distilled ether, then evaporate the ether fraction to 1ml,then do HPLC, but the column and retention time is different from that for acidic hormones.
You have to collect the necessary mass of plant parts that you want to analyze. Cytokinins can be quantified with HPLC/MS while 2D-HPLC is most suitable for auxins. Please refer to: Dobrev and Kaminek (2002); Dobrev et al. (2005).