I just hauled a few kayaks with my 3rd gen factory roof bars. They make attachments to put on the front crossbar to raise the front of the boat up so it doesn't rest on the sunroof deflector. I couldn't find mine, so I just rolled up towels to wedge underneath, and it did the job. Heres a pic of mine.
3rd Gen T4R Picture Gallery
I would love a baja rack or surco rack, but this works for now. If putting the canoe up there is all you need it for, I would save the 300-400 bucks for a rack. If you want it for looks too, well that's a different story...
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2000 Limited, 2wd, auto, 3.4, 265/75/16 Hankook Dynapro ATM RF10