Here's a sticky that we had on the question of Neem oil and beneficial insects including bees:
Bottom line is that Neem oil does not kill on contact, it only kills if ingested. So mainly it only kills leaf eaters. That means it is less effective for sucking insects like aphids and stinkbugs, but it also means that it is not harmful for beneficial predators, like the predatory wasps that keep the hornworms and other things under control. Honeybees are a little bit in between, because they do ingest pollen. They don't seem to be harmed by small quantities, but given their vulnerable status these days, if you can keep the oil off the pollen, that is probably a good thing. You could still spray the leaves of flowering plants, if you do it without blanketing the plant.