I'd go with the last suggestion, assuming that you hold passports that allow your wife & son to visit for as long as you would like during the year.
Immigration obviously sees when you go in and out, so applying for an extnsion claiming that your wife had been resident here for a year when in fact she just visited once or twice for a few days opens up potential issues.
But also why not email Immigration and ask their advice - it's not like you're trying to do something tricky here. Simply tell them that unfortunately your wife will not be able to join you as soon as planned and ask their advice on how to handle the visas.
enquiry@immd.gov.hk