First piece of advice: Sending out a cover letter with no reel to back it up is a big no-no. You’ve already lost your audience, the hiring manager. Imagine being a girl scout selling cookies, but actually having none in stock or any idea what types you might carry. You can kiss that sale goodbye. Get those ducks in a row before you apply. Right now, somebody is taking the job that might otherwise have been yours had you been ready to present.
Second piece advice: Know your target audience. Matte work can cover a variety of genres. Aim for a diverse, varied, and interesting mix of environments. Show that you also know the material. Not all mattes are hand painted. Some use a mix of CG and photo reference. A perfect example might be how some movies turn modern New York into its 1920s equivalent or some stylized version. Elements are removed. New bits are added. Weather is changed. You can see quite a lot of this on TV shows like Gotham where they build mattes to turn NY into Gotham. You also see it in films where they turn modern New Zealand into some Tolkien-type land of myth.
As far as paper size goes… Digital. Having a physical portfolio to carry around with you is great… as an option. However, digital is the first point of reference for employers. They can see how you break down a project in detailed fashion. You can also add/remove material from rotation as necessary or desired. Always current. Size-wise, 11x17 is fine enough to carry around. Manageable, but not too small. I used to carry around these near poster sized Fuji & Kodak approvals/prints that were just so cumbersome. Never again.
As you well know, there are added issues with working in print and going from digital. Color space changing and correction can sometimes be tricky. A rushed or bad job can turn a great piece into a bad one in an instant. Ink, stock, and actual printer can destroy a good work if you’re not careful too. It’s a juggling act. Again, I’m sure that you know this stuff. I just thought it was worth mentioning. I screwed myself over like this a few times in the early days. Now I know better.
On a personal note, I like breakdowns. We often take these mattes for granted. Being able to see how the impossible became reality can be a real eye opener and give me newfound respect for the artist. You don’t necessarily want to do this for every piece, but showing off and flexing your muscles with a few can give employers an insight into your process and habits.
EDIT>>> Here’s a Gotham related matte reel so that you can get an idea: http://www.cgmeetup.net/home/gotham-matte-painting-and-environment-reel/