>1) mark boxes from a given apiary, extract them in series and sample the
honey in the sump ½ way >through extracting the apiary.

>2) during the spring inspection, take a syringe and partially fill it with
honey from the brood >nest of each colony in the apiary (or a subsample).

>Any other ideas?

It would depend on how much honey you need for a sample. If only a small
amount was needed I would use a sterile cotton swap to puncture a capped
honey cell. Then put the swab(s) into a sealed and labeled plastic bag.