While all islands that have bareboat bases are accessible by air, sometimes it's easier or less costly to fly into another island then get there by ferry. In the Virgin Islands, for example, there are many more flights into St Thomas USVI than into Tortola BVI, and the flights to Totola may be sold out. Or, you might be able to get frequent-flyer awards to St Thomas but not to Tortola.
In either case, you can fly into St Thomas and take a ferry to Tortola, if that is where your bareboat company is located. While ferry service is reasonably reliable in the Virgin Islands, be aware that schedules are "subject to adjustment" which means a particular trip might be cancelled on fairly short notice. It's always best to phone ahead to make sure that the ferry is going to run. As there are two competing ferry companies, Native Son and Smith's Ferry, the chance of not getting from one island to the other about when you want to is fairly remote.
Do bear in mind that on the day your charter ends, you might have to take an early ferry back to St Thomas in order to be sure of making your flight home. If the ferry takes you into Red Hook, you still have a 45 minute ride to the airport. eBare.com generally recommends flying into Tortola rather than St Thomas if you are sailing with a BVI-based company.
Click Here for Virgin Islands ferry schedule
If you're chartering with Tradewinds in the Grenadines, you'll probably find it easier to fly into St Vincent and take a ferry over to Bequia, than to fly into Bequia, which is only accessible to small planes.
Click here for St Vincent-Bequia ferry schedule