If you are just starting with limited capital I would try Just2Trade, they offer stock trades at $2.5 a trade or $2 if you have an account size of 50k or more. You will need a charting platform though such as Quotetracker and use Just2Trade data to feed it, you can also execute trades via QT. I have been a customer of Just2Trade for a few months and their customer support via phone is very good for such a discount broker. They have the lowest margin rates in the industry and offer about 4.25% on the money market account. Sorry, missed the intention of the poster, Just2Trade do have an API platform but never used it to automate trades.
especially with automated systems, make sure you choose a firm with some support as well. Commissions are important, but one problem can cost you a lot of money if there is not support. From what i read, Global Futures sounds cheapest, if comm is all you're concerned with, but i don't like the monthly fee. If you're volume is above 1000 rts/month, velocity offers better rates. I wouldn't recommend IB. Glad to hear you're not pushing the $300/contract margin, that's insane.