I have spent the last few months querying agents about my latest manuscript. As you research agents one of the important things to note is whether they like to receive their queries by email or by letter.
Many offices are trying to go paperless and only want to receive emails. If this is the case, then you don't really have a choice, send that email. Be careful to follow their submission guidelines. Some agents like attachments while others want everything included in the text.
In my opinion, I like snail mail. If an agent or editor doesn't have a preference, I send it by post. Why? In my experience you are more likely to get a response, good or bad, through the mail. I'd say 50% of people I've emailed don't bother getting back to me. They're very busy and sometimes only respond to people they are interested in. However, this leaves the writer in limbo. You wonder, did they even get it? Should I resend? What did they think? Sometimes a year down the road you get a reply, wow!
With snail mail you have the option of sending a SASE. I love these. I've received three back in the last two weeks, all rejections :(, but at least I know. The agents simply sent a standard postcard or returned my query with a note on it. It feels great to know they took the time to look at it even if they rejected in the end.
Either way your left checking either your mailbox or your inbox everyday. That at least doesn't change.