Hmmm... that depends on the particular lens. Generally, the very BEST optics are manufactured by both Nikon & Canon, and these are superior to anything made by Sigma, Tokina, Tamron - but we're talking about the very expensive optics here, lenses costing well over your entire budget. For the lower end stuff (like your 70-210mm, 70-300mm etc.) it's a bit nip and tuck. That is to say, certain 3rd party (Sigma, Tamron, Tokina etc.) lenses are superior in optical quality to their Nikon/Canon equivalents, and in other cases, the main manufacturers win out. Canon have a certain handling advantage though, in that many of their lenses use USM focusing mechanisms (which is near silent, and faster than conventional autofocus lenses). Nikon offer that on only a few very expensive lenses, as do Sigma (Nikon's version is called AF-S, Sigma's is called HSM).
$1000 would probably just about buy you a Canon EOS 30 (or 33 - the only difference is whether or not you want eye-controlled focusing), and Canon's 75-300 with Image Stabiliser. (I don't know what the US equivalent name of this camera is, I THINK it's the Elan 7 (anyone help me out here?)) If you buy the non-IS version of this lens, you'll save yourself $300. If you would prefer to go the Nikon route, you'll be looking at the F80 (N80), and probably Nikon's 70-300. Each way has its own advantages and disadvantages, but the best advice (as Colin suggested) would be to go into a local camera store, and try out the cameras to see which one you prefer before choosing.