I've used both services but in my case they are both one stop with short flights.
-The seat itself I prefer ACA over ANA as you get more shoulder room on ACA. ACA's leg room is less but I'm short, wide at the shoulders and narrow at the waist so I prioritize leg room less then shoulder room.
-In terms of the staff ANA beats ACA hands down and ANA has better food and drinks.
-ACA selection of movies is more western oriented if you do not want to read subtitles, if you don't care and want a broader choice go with ANA.
-Travel time as people have mentioned can vary massively depending where you are staying. If I am on my dime I usually stay at the Best Western Shinjuku and it is actually more convenient and only a bit longer to fly into NRT and take the N'EX. That train has spots of luggage plus I don't have to connect. The Tokyo monorail does have luggage spots kinda but after that a big bag will be a nightmare on the other trains. If it is for work they toss me into the Hotel Okura Tokyo and taking the trains from NRT is a massive pain, and you basically need to take the limo bus.

In either case if you have a big bag I would highly recommend dropping it off at Yamato and have them deliver it to your hotel the next day. I pulled a WT 30" through Shinjuku station once and I will never do that again.

If you were paying cash I would say to take the JAL 787-8 with the new Skywider II seats.