I guess it depends on both what city/region the LFS is located in and what online sites you price/purchase frags on...
I've purchased frags from a few LFSs here in the greater Washington D.C. area and their sale prices are about the same or just a touch higher than the prices online shops.
For example, I purchase a nice, nickle-sized goniopora frag (probably ~15 heads) from the LFS for $40 on sale. A week later I found a prettier, fuller quarter-sized goni frag for $30 in weekly sale that AquaSD holds on another popular forum.
Just one example...
All in all, if they're on sale, the prices and quality of the frags at the LFSs here can be about in the ballpark with those online - sometimes a little prettier and a few dollars less, sometimes not quite as pretty and few dollars more.
When they aren't on sale, the LFS frags around here tend to be quite a bit more expensive than those I can find online.
Of course, the general cost of living in this area can be a bit higher on some consumer goods than, say, northeast PA where I grew up. So a frag in a LFS that sells for $40 around here may very well sell for $10 or $15 less up there.
I will say this though, the frags I have gotten from my preferred online vendor have always proven to be cleaner (e.g. far more pest free) then those I've purchased locally. But that's something that is naturally dependent on the practices of each individual vendor regardless of whether they're local or online.