We recently partnered with a company called Giact, and in my experience they are the best check drafting company I have ever seen. We also personally use them for our own drafting. Their system gives you a online virtual terminal, and there is an API available if you want to integrate check drafting into your website. The best thing about them, is that they don't use the ACH system, disputes are extremely difficult compared to ACH where only a phone call is required, and the funds are transferred much more timely / reliably compared to ACH.