For comparisons sake, I did the AG Surly Bender from Northern Brewer and it turned out great, so I used that recipe on Brewbuilder from Brewmasters Warehouse.
Northern Brewer(no yeast): $26.99
Brewmaster's Warehouse(no yeast): $29.11, but using the 10% off code for the Brewing Network, you get $26.19
My LHBS is a little pricey, so it would all come down to shipping for me. The Pro Series kits are supposed to be using the exact ingredients, so Brewmaster's Warehouse doesn't carry the base malt for the beer, so I just subsituted for it.
I would say it is a wash either way, but if you want to support NB, then go for it.