I'm assuming you have wifi, the wii u player has to go to a multiplayer tavern in Tanzia, then the 3ds user talks to Neko and does a Friend Search. Should find the wii u player, and voila enter the same area.
Which option? The multiplayer port? I think you've just gotta make sure the 3DS player's using friend search. But I was a 3DS player last time I was doing it, so I don't know that much about what the Wii U player's supposed to do.
Make sure the Wii U player goes into the multiplayer local play of Tanzia port and not network play.
The 3DS player will need to talk to the cat and do a friend search, or if you're in the port/tavern, go the next area (i.e, in the port and move into tavern) and press X instead of A so you can fast travel and use friend search.
hang on, you guys are like, in the same room right? The 3ds can't connect to the internet like the wii U can, so you have to be together if you want to play together. (no real info was given so just in case)
the wii u is basically exactly the same as the 3ds version, the instruction manual for the Wii U version tells you how to connect a wii u and 3ds together, thats how me and my cousin figured out how to play together. i have the 3ds version.