Which has better efficiency: step-up or step-down switching voltage regulator?
Boost converters are typically less efficient than Buck converters, but not by much.  The fundamental reason has to do with the inductor current flowing directly to ground during the on-time, instead of through the load, like it does on Buck converters.  There is an EE-Times article that mentions this: Unscrambling the power losses in switching boost converters


  Generally, however, since inductor current flows to ground during the
  on time, only a fraction (off time to period ratio) flows to the
  output, as illustrated by the pulsing currents in Figure 2 (this is
  the reason why boost converters are generally less power efficient
  than buck converters)




Since the efficiency differences are not significant, you are probably better served deciding on additional criteria instead of regulator efficiency alone, including:


Charger complexity (single cell is simpler).
Cost
Size
Cells in series will be limited by their weakest cell.
Cells in parallel tend to charge one another, and there is an efficiency hit due to the chemical process.
Losses due to higher input current with lower voltages (parallel cells).