I've done BOS <-> HKG on Cathay in J and BOS <-> NRT on JAL in J several times each. Overall, I think I like the Cathay product a tiny bit more.

As far as the seat goes, both are pretty good, but I like Cathay's a bit more. It's got a bit more space, you're a bit further from the other people (due to the design), it has some more storage, and I find it to be generally a bit better laid out. Overall, they are both quite nice, though.

For service, both airlines are top-notch. Though I generally find that Cathay's flights between HKG and BOS are less crowded in J and therefore the service is a little better just because they don't have as many passengers to attend to.

For food, I personally like the food better on Cathay, but I like that JAL offers their second meal as anytime dining. They are both pretty good, though. Cathay seems to be quicker about the meal service, which I personally like.

For stuff on the ground, HKG has the slightly superior lounges. NRT's Sakura Lounges are good, though, and I never seem to encounter the crowds people in this thread mentioned. In BOS, they both share access to the BA lounge, which is nothing special -- it's a comfy place to sit, but that's about it.