Start by asking your manager if there's a reason why he chose Comic Sans.
Hey John, I noticed that you write your emails in Comic Sans font. Is there some specific reason you picked that font?
Most likely, he would respond with, "no specific reason", "it looked good", "my secretary configured it", etc.
Then continue with this:
I read an interesting article the other day, which said that Comic Sans has a mixed reputation in the business. I wonder what our client thinks about it, perhaps they don't care, but just thought I should let you know.
This gets the message across, doesn't sound condescending, ensures that your manager doesn't lose face, and also saves you from the awkwardness of "recommending" a font to your superior, because you are putting the decision in his hands. If your manager is a reasonable person, it is hard to imagine him taking offence to this, especially since you offered to first understand his reason rather than just pass judgement. :)
In addition, it also lets you save face if the manager has some genuine reason. For example, if the font was the default on his computer and he hasn't figured out how to change it, or the client "likes" that font!
PS: As David K pointed out in the comment, you might want to keep such an article handy. Make sure that it is from a reputed source, not a random blog, and don't send it to your manager unless he insists.