When doing this, however, you have to be very careful with the job description - the CBP manual specifically excludes programmers from the CSA definition. CSAs can do some programming as a part of their job, but that cannot be their principal function. If your cofounder has an engineering degree (and is a EIT), they may be able to get a TN-1 under the much-broader classification of "engineer".
That said, there are any number of valid ways. If they're not taking a salary from the startup, for now they can enter on a basic business visa (B2 I believe) while they "explore opportunities", but they cannot make any money from a US source. If they are making money, you may be able to get them a basic employment visa. You might also be able to set up a Canadian corporation and they can be a transfer from one entity to the other. If they have enough money they can get an investor visa (E2 I think, takes anywhere from $500k - $1M)... Like I said, there are a huge number of different options, only a lawyer can advise you on which one is best/easiest/most appropriate.