There are pros and cons both ways. In my city, we have Petco and 1 LFS that sells saltwater fish currently. Petco's prices are right, but their fish are always sick...hence I don't want to buy there. At the LFS, however, their fish are healthy, but their prices are so high it is outrageous.
2 Clownfish at LFS at 35.99 = 71.98 plus tax.
2 Clownfish at LiveAquaria.com at 13.99 = 27.98 + 30 shipping = 57.98.
You might save some money buying online in the long run, not to mention the much larger selection online...but you don't get to see the fish and how they look or see if they are eating...I looked at almost 20 Coral Beauty Angels locally before I found that perfect one I wanted to take home and then watched him eat voraciously...an advantage you lose online.
You have to weigh the pros and cons of both methods and decide for yourself.