Haha, wow. If someone wants to pay me $400,000 for this website I think I'd take the money and run!
But no, I think the fact that one site says $400,000 and another says $9,000 goes to show how unreliable the figures are.
They are usually based on number of visitors. We are very popular right now because of Black & White so things are probably higher than normal. But a website is only worth what someone is willing to pay... and I don't think anyone would pay for a Pokemon website.
EDIT: I found a few 'calculators' online and they say $40-50k. But they are WAY off on the page views. They say 25,000 page views/day, but before B/W we had around 300,000. Now it's over a million. My mind boggles.