Depends on what is your preference. Fuji-Q Highland is for people who love extreme rides - many roller coaster rides and their haunted house is pretty scary too. On good days, you can see Mt. Fuji from Fuji-Q Highland.
DisneySea is the adult counterpart of Disneyland. They have more action rides but not too scary (nothing near Fuji-Q's roller coasters). You'll get to have a better look at the night show as well because it's localised in the middle of the park. Disneyland is more "fairytale" and "magical", obviously geared towards kids. Rides are mild but you'll feel like you've travelled back to your childhood. In terms of meeting the characters, I feel that it's easier in DisneySea (based on my personal experience). Out of the two parks, I prefer DisneySea (the food is more to my liking too) and I've been there more than once, as compared to DisneyLand.
Fuji-Q is great for all roller coaster buffs with an awesome view of Mt. Fuji. If you've never been to Disney, you should check out both parks. But, if I were to recommend one, it would be DisneySea. You must ride Journey to the Center of the Earth since its a unique ride to Japan! Take advantage of FastPass to ensure you'll get on it. If you'd like to see what a 1-Day experience looks like at DisneySea, you can view the 1-minute video that is published here on JapanTravel!
Disneyland is ideal if you have kids below 12. Disneysea is ideal for teenagers, high schoolers and lovers. Disneysea is only in Japan. In the US, they have the Water World and some claimed it's just similar to the Disney Sea, but I totally disagree.
Fuji-Q is ideal for active and adventurous teens and adults who can go for extreme rides. Let me add, Universal Studio Japan, it is ideal if you are crazy over Harry Potter and other motion pictures movies. If you want less extreme but adventurous rides, USJ is great.