On the other hand I don't want to sound rude or look like I'm not putting effort into an area.
You are right to worry about that. If you're responding to a published "jobs" email address, whoever sifts through that is likely to have lots of messages, many from people who are not qualified but are sending applications to every jobs address they can find. You don't want to look like one of them.
So, unless the job ad specifically instructed otherwise ("send cover letter as an attachment"), the email body should be the cover letter, with the resume attached. Don't make the recipient open an attachment just to find out if you're even vaguely interesting; that makes you easier to ignore (or set aside for later, and then "later" never comes -- I've definitely done that with email that's inconvenient right now, e.g. because I'm reading it on my phone). Make the email compelling enough that the reader will want to open the attachment, your resume.
It's often said that recruiters and HR screeners spend less than a minute (perhaps well less than half a minute) looking at the average resume. With emailed applications, isn't it reasonable to assume that the clock starts running when they open your email? I've found it best to put my pitch right there in the first lines of the message they've already opened -- draw the reader in and you raise the chances that yours will be one he spends more than 30 seconds on.
In addition to making it easier for the reader to see how wonderful a fit you are, by using the message body effectively you demonstrate that you are resourceful enough to use the tools you have to best advantage. I doubt that anybody cares about a nicely-formatted PDF cover letter; just give 'em the payload, the actual information, up front.
(This answer is drawn from experience as a job-hunter and anecdotal evidence from HR folks at companies where I've worked. I'm not an HR person or a recruiter.)