Ok. I didn't realize you were actually talking about following a 12+ hour flight with a 5+ hour train trip without a night in between.

Arriving at NRT in the afternoon, the fastest train connections to get to Kanazawa the same day involve 5.5 to 6.5 hours, 2 or 3 train changes and getting into Kanazawa sometime between 10:00 pm and midnight. The shortest times assume you can navigate Tokyo Station at the height of the rush hour in under 15 minutes, not a guaranteed proposition unless you are pretty familiar. Otherwise, 6 to 6.5 hours. And good luck with the jetlag at your conference the next morning.

Arriving at KIX, the times are about 3.5 hours with one change at ShinOsaka. Much, much easier and faster. But, as others have mentioned, the connections just to get to KIX from the east coast are rather daunting. Every airline except UA connects in NRT for KIX anyway. Might as well just get off at NRT and go from there. UA connects in SFO and then goes direct to KIX but you are looking at 6+ hours to SFO, <2 hours layover and then 12+ hours to KIX. Then 3.5 hours on the train to Kanazawa. Are you sure you can't leave a day earlier, make the connections easier with a night in SFO or KIX/Osaka/Kyoto or NRT/Tokyo and give yourself a little downtime to decompress before jumping right into your event? Just sayin'.

For air, the closest airport to Kanazawa is Komatsu (KMQ.) The only airline that flies there from NRT that I can find is ANA. JAL flies there from HND but that would just add a whole lot more hassles and time than it would be worth. The single flight fares seem kind of high but if you are flying ANA or other Star Alliance carrier you might be able to add a NRT-KMQ segment at reasonable cost. It looks like they have a 7:30 pm flight that gets to KMQ at 8:50 pm. Of course, you then have to get from Komatsu to Kanazawa. I guess a cab to Komatsu Station and a <20 minute ride on the Limited Express, getting in around 9:30-10:30 pm. Kind of a wash for time. Looking at ITA, it seems that every airline combination from BOS winds up connecting to that same 7:30 pm ANA flight from NRT-KMQ except JAL.

Good luck.

EDIT: I like jib-san's suggestion to fly to SFO the night before, spend a comfortable night in San Fran and fly out on the late morning departure to KIX. Makes for a much easier trip.