Part of the pricing is based on supply and demand.
I suspect the demand in Boston and Atlanta will be similar. The supply is totally different, however.
TD Garden's capacity is only 18,624
Over at the Georgia Dome "the clerk told me that they were setting up for 40,000".
I just checked some pictures that I took from last year's SEC championship game. Those show that the upper deck was not utilized. UK fans report having tickets in the upper deck for this year's regional.
Wikipedia claims a capacity of "53,000 for basketball when the dome is fully open and 40,000 for basketball ... when the dome is sectioned off". I suspect they may try to outdo the 53,000 figure for next year's Final Four and attempt a new Final Four record. We'll see if this year's edition will outdo the previous record. One has to believe that 2014 will set a record that will likely stand for a long, long time.
Here's an overview of Final Four attendance records and recent figures:
1987 64,959 Super Dome
2009 72,456 Ford Field (semi final)
2010 70,930 Lucas Oil Stadium
2011 70,376 Reliant Stadium
2012 ??,??? Super Dome
2013 ??,??? Georgia Dome
2014 !!,!!! Arlington - Jerry World