I have been to Israel three times but always on a cruise, so booked the excursions through the ship. It has to be one of my favourite places though. Maybe Windstar will offer some pre cruise land tours ?
Things to see-Dead sea - Nazareth-Bethlehem-Jerusalem-Wailing wall-Sea of Galilee-Gardens etc etc.
The tours are a fair way from the dock and full day though ! Not sure it would be very easy independantly.