I am building an application that will have a number of notifications going out via email. Is there a guideline on making the content of the email accessible to screen readers and other similar tools?
Maybe a bit late for you, but your question is still relevant today. You can start with W.c.a.g. guidelines, but keep in mind not everything is applicable in email.
The email accessibility checker I developed is optimized for email HTML, and may be easier to use: http://www.accessible-email.org
It tests your email for different accessibility feautures which are possible in email and it will tell you what accessibility features are missing. (if any)