Carpenter bees can be a nuisance as they eat the honeydew from aphids and scale insects. Honeybees are not aggressive, so there is no need to kill them unless you have an abundance of carpenter bee nests in your yard. The best time to do this will vary depending on where you live and how abundant the carpenter bee population is in your area. Carpenter bees tend to nest near trees, so if you find large numbers nesting under the trunk of a tree or along its edge then it may be prudent to call a professional exterminator that deals with these species for additional help dealing with them.
If there are only small numbers of carpenter bees around than waiting until spring when they emerge from their underground tunnels will usually work just fine for killing them off or at least making sure that none survive long enough into summer season before we take care of those last ones once again. For more information about how and when Carpenter Bees emerge follow this link: How To Identify And Kill A Carpenter Bee