If you put the text before anything else, it would be displayed nicely in html-off viewers but would not be nice in HTML mails. On the other hand if you format this text with HTML, it would be nice in HTML mails but other users will see it in HTML too.
I personally prefer to warn the users not in the email but in the screen where they choose to receive HTML mails. It's why I included the hack the special link part to switch user mail option (the part you can change your mail setting with one click without going into your usercp). I add the "click here to get HTML mails" link to normal (non-HTML) email notification template and if the user clicks it, their settings change but they also get a detail warning about the effects of the this change (get garbage mails) and how to correct it if they encounter these effects (go to user cp and revert back to text mails). My board is not a large one but it seems to work for now. I havent got even one complaint from the members that they cant "read" the mails.
This is my way of dealing with HTML mails, use it if it fits to you too