: I'm thinking about building my first kayak,

FANTASTIC! Just a word of caution: IT'S ADDICTING!

: no real woodworking experience.

You really won't need much. The two tools you'll use the most are a jigsaw and a sander. What you really need is epoxy and fiberglass experience.

: I've been looking at Pygmy's Artic Tern and CLC's Chesapeake 17LT.

Two great choices, but are you sure that either of these designs will fit the majority of your paddling needs. There are always compromises that must be made to decide which boat "fits the bill".

: Are there any advantages to glassing the inside also rather
: than just tape?

Both methods work fine, but I believe they both glass the inside of the cockpit area. I think, that glassing the entire inside is a good idea, but it could be done with either of these designs. It does, however, add some difficulty to the project, but is a good place to practice with glass/epoxy. Tape is easier. Either will work.

: Also, I think Pygmy uses butt joints, and CLC uses scarf
: joints, is one better than the other?

No. At least I don't think so. It's been discussed here many times. Check out the method that Vaclav at One Ocean Kayak uses : http://www.oneoceankayaks.com/stitchglue/plyshophtm/scarfjig2.htm
He uses a jig to cut the scarf with a circular saw. I've done it and it works great. Scarfing the plywood can be intimidating for someone that hasn't done it before, but it shouldn't be, just take your time and make sure it's right before the epoxy hardens completely.

: Any advice on these topics, or if
: you prefer Pygmy or CLC and why, or if anyone has any experience building
: from either of these companies, I'd really appreciate the advice
: Thanks!

I chose the Chesapeake 16 for my first (full sized) boat and built it from the book "The New Kayak Shop". I couldn't recommend it higher. Great book. The main differences that I see with the two "big boys" are that CLC offers plans for most, if not all, of their designs, while Pygmy forces you to buy a kit. In my opinion, you don't need a kit unless you're in some kind of hurry. For the kit price, you can build two from scratch. The books and plans, together with this site offer way more than you'll ever need to build a stitch'n glue boat. Consider building a small model first, from scratch, just to get the hang of it. Order an epoxy sample to play with on scraps etc... Once you have a grasp of all of the tasks involved, and you gain experience with each task, you'll develop your own methods, that quite often are a combination of how others do it. Then, right when you feel comfortable with one method, someone will shed some light on a whole new concept.
Don't rule out the strip deck hybrid. Great alternative to the ply deck, and you'll gain strip building experience at the same time. For this method, you'll also need Nick's Book "The Strip-Built Sea Kayak". Follow Chris's book until you finish the hull, then switch to Nick's book to build the deck. I would recommend reading both books cover to cover even if you go with Pygmy. In the end, it's your choice and one thing I've learned is that there is no perfect choice, just do like I do, and make a list. Too many boats, not enough time.
Smf