It's a big island even if you have a car.
I'd stay in Pythagorio or Samos Town - both are large
enough to give you lots to do and both have a good
selection of hotels.
Pythagorio is the prettiest (IMHO) and you can catch
a ferry to some of the tiny islands for a day trip.
Samos Town has a GREAT little museum - really worth
a few hours.
We were there after a tour that ended the second
week in October and outside of the two towns a
lot of things were winding down; 'end of season'
was a common comment!
We rented a studio for two weeks but stayed at the
Samos hotel b4 catching the ferry back to Turkey.
V. nice hotel with a lovel roof-top plunge pool
and view over the harbour.
Manolates is a lovely little hilltop village but
you either hike or drive up a mountain to get there.