There's no more difference in intelligence between labs of different colours as there is between people with different colour hair. It's impossible to make such a sweeping statement.
There is a massive difference in intelligence between different labs though - particularly between trial bred, working bred and show bred dogs. As a rule of thumb, I have found that 'brightness' in types if labs runs in that order. Brightness isn't the same as intelligence though - there are some very, very bright labs who have not a single grain of drive, instinct or common sense.
Soggy has hit the nail on the head; it is down to how they're bred - and lab history. The default colour for Labradors is black and for a long time black was the only desirable colour. Yellow and chocolate dogs weren't seen as desirable until a good 100 years after the introducton of the breed.
Colour of the Labrador coat is determined by their genes - and simplistically speaking there have to be two matched genes from their parents to produce any colour. For a long time, the gene pool for chocolates was quite small and as the colour became very fashionable lots of pretty crappy breeders bred for colour alone. Without considering the overall dog.
It is possible to test labs for colour genes - and there is now a greater understanding of how the colour bit works so the chocolate pool has been carefully and skillfully expanded to produce good all round chocolates again.
For example one of my breeding bitches is black and she carries a chocolate gene - so if I mated her to a dog who is chocolate carrying chocolate, she would produce all chocolate puppies because HER black gene has nothing to match up to.
If I mated her to a black carrying yellow, or a black carrying black dog we would get all black pups because she doesn't have a yellow gene to pair up with the yellow gene, there's no incoming chocolate gene to match up with hers and so everything will default back to black.
With all that in mind, brains just can't be defined by cost colour. It is down to the parents, grand-parents and on and on backwards.
Fashion in dog breeds has a lot to answer for, both in pedigree dogs and currently in bollocking stupid 'designer' mongrels. Fashion creates an opportunity for the unskilled and unscrupulous to churn out dogs with regard only for the cash they can pocket. I have a bit of an issue 
.