How do I select the best transformer/regulator strategy?
Option 1 Use a 5v 3A DC PSU and step-up the voltage to 6v using
  something like an LM2621 step-up converter. These apparently are 90%
  efficient typically and a pretty cheap.
  
  Option 2 Use a higher voltage DC PSU and step-down the voltage to
  power the RPi. A linear regulator will be inefficient (and hot) and a
  switching regulator is more expensive.


You are contradicting your requirements. Option 1 using a step-up device IS likely to be using a switching regulator. This contradicts option 2 that assumes a switching regulator is expensive.

It comes down to this. Using a switching regulator in either step-down (buck mode) or step-up (boost mode) will give minimal power dissipation. If cost appears to be a factor look at the cheapest (or most available) wall-wart and if it's 12 volt then use a buck (step-down) switcher. If it's 5V then step this up to somewhere between 6V and 12V using a boost switcher.

The LM2621 is fairly cheap but if you look into there range of "simple switchers" you'll find a buck regulator that matches the price at a bill of material level for sure.