I agree with other folks, I would steer towards three pin, just because you have a lot more variety. I use a NNN BC boot with Atomic Rainiers, and regret that choice. The boots aren't bad, but they don't seem to fit my feet really well. Since there aren't many NNN BC boots, I'm kind of stuck. If I had three pin, I would experiment more. Plus, if I wanted to get a much heavier boot, I could. The main thing, though, is that I would start with the boot. If you go to the store and find that the NNN BC (or SNS BC) boot fits really well, then go for it.
Regardless of what you get, it is unlikely to be your only pair of skis. The terrain and the conditions are just too varied to rely on one pair of skis (I say that not having skied in the Sierras, but having hiked in them). I ski in the Cascades (which has terrain that is even more varied) but I think the general rules apply. Having different sets of gear (matching skis and boots) allows you to pick the right gear for the terrain and the conditions. I have the following:
1) Really skinny, long, light skis paired with SNS boots for groomed or very light backcountry.
2) Fischer Outbound Crown (no metal edges, 10 mm sidecut, decent flotation, fairly short for Nordic) and the same boots for light touring under good conditions.
3) Atomic Rainier (metal edges, more sidecut) and NNN BC boots for tougher back country and icy conditions.
I stop there, but my brother starts there. I wish I could remember what gear he has, but as you can imagine, he has heavier boots, along with curvier skis. I simply don't attempt a lot of things he does (or I just slop my way down the hill while he carves his way elegantly).
If you haven't already, I would try and find copies of Ski Tours in the Sierra Nevada by Marcus Libkind. Just the cover of Volume 1 (Lake Tahoe) had me salivating. That is my kind of skiing (moderate grade, no road). I think the books are out of print (although you may be able to find copies somewhere) but he has basically copied all of the information on his website.